Sheppard's Pi
by Evergreen
Summary: Colonel John Sheppard's been shifted backwards, forwards, and in between time and dimension on Atlantis. CHAPTERS 13 NOW UP. Nothing is as it seems. Patience will be rewarded. Much Shep whumping.
1. Chapter 1

**Sheppard's Pi**

**By Evergreen**

**SUMMARY: Two years after the first Wraith attack finds Atlantis and her crew in a very different place. The only problem is that John Sheppard doesn't remember any of it! **

Major John Sheppard woke up suddenly as if from a bad dream, but he couldn't seem to recall it as he sat up in bed. His eyes quickly scanned his dim surroundings and ascertained that he was, in fact, not in any immediate danger. He was about to roll over and go back to sleep when he noticed that something had moved and was now pressing up to his right leg. He leapt out of the bed, heart pounding, in order to face his "foe". He backed up slowly towards the door and willed the light switch to turn back on. His eyes settled back onto the bed to determine his adversary to see that it was Teyla!

"Teyla?" John exclaimed and he stumbled backward out of the room. _How did that happen? _He thought he heard Teyla calling after him as the door slid shut. He had absolutely no recollection of asking Teyla to share his bed that evening. He shook his head in an effort to clear it. He also didn't remember, or feel like, he had been drinking heavily enough to warrant his blanking out. He looked down at his state of clothing and noticed that he was only wearing his pajama pants. He walked slowly towards the end of the hallway, desperately trying to remember what had happened last night. His head started to buzz with the effort. He decided to head towards the locker room to score a shirt at least and something to put on his bare feet. As he walked towards his destination, he began to notice his surroundings. The lights in the hallway seemed to glow a little brighter than he remembered. _Probably just my imagination_. All the electronic displays lit up for him as he passed as usual, so he just sighed and kept walking. No one was in the hallway or in the locker room as he entered. He padded over to his locker and proceeded to enter the combination into the keypad. It buzzed at him several times before he gave up in disgust. Things were getting just a little too _"Twilight Zone_" for him.

His fingers went up to his right ear to engage his comm., when he realized that he hadn't grabbed it during his hasty exit. He shook his head and decided to head back to his room and talk to Teyla. Perhaps she would understand what was going on. He was hit with his first wave of vertigo about halfway back to his quarters and slammed up against the wall to prevent himself from falling down completely. It passed quickly and he decided to move a little faster to make it back to his quarters before anything else happened. He was about to trigger the door on his quarters when it slid open to reveal a puzzled-looking Teyla. And as if a huge hand shoved at him from the front, John Sheppard was swept to the floor and into darkness.

"Colonel, can you hear me? It's Dr. Beckett. Open your eyes if you can." The Scottish brogue of the station's doctor brought John back to the surface of consciousness.

"Yeah, yeah. It's still Major to you, Doctor." He opened his eyes and started to sit up when the sudden feeling of lightness in his head stopped him. "Whoa. I think that I'll just lie right on back down. Man, I feel like crap."

"I know…John. I'm just glad you're awake again. You've been in and out of consciousness many times over the last couple of days. How do you feel exactly?" The doctor flashed a bright light into John's eyes as he asked the question.

"I feel as if my head is not really connected to the rest of me, like it's floating a few inches above my shoulders, if you know what I mean. I have a roaring headache and my stomach's not very happy with me right now. How's that?" John stared back at the ceiling.

"I ran some tests and I'm still not entirely sure what's going on with you. No one else has presented with the same symptoms and I can't find any evidence of disease. What's the last thing you remember?" Dr. Beckett was making a few notes in John's medical file. A few people wandered around the infirmary, but there didn't see to be anyone else actually requiring medical attention.

"I was just getting ready to deliver the nuclear device to one of the Wraith motherships…then waking up next to Teyla just a little while ago…," he trailed off in an effort to gauge the Doctor's reaction. Dr. Beckett did not flinch, react, or even look up at John's admission. He closed his mouth and waited.

"Wraith attack?…Anything else?" Beckett looked back at John, purposely hiding his emotions at his response.

"No, I think that's about it. Obviously, it went well or we all wouldn't be here. Have all the Wraith been eliminated from the city? Any casualities? Damage to the city?…I need to talk to Elizabeth.." John started to get out of bed and then stopped as he observed the expression on the Doctor's face. "Why? Is there something else I should know?" He looked directly at the doctor, trying to figure out what was wrong.

"It's just a question." The doctor put down his notes gently pushed John back into a supine position on the bed. "John, this may sound like a really stupid question to you, but what year is it?"

"It's 2005, earth time, of course." John closed his eyes and waited for a response against what he was sure was _not_ what he was expected to say. He was also sure that the doctor was hiding something from him. "Are the Wraith gone? I can't seem to recall how things ended with them."

"John, it's 2007, Earth time. The Wraith have been defeated for about a year or so. You were promoted to the rank of Lt. Colonel after the Wraith attack and you had returned to Earth."

"Are you kidding? Promoted…Returned to Earth…You're kidding me. Am I hallucinating again, like on that planet with the mist people? Did McKay put you up to this? Just how much did I drink last night?" John tried to sit up again and valiantly attempted to fight the vertigo that washed over him again. He groaned and closed his eyes.

"Just rest. I will talk to you again in a little while. Try not to think about it too much." Dr. Beckett pressed his fingers to his comm. device and called Dr. Elizabeth Weir to let her know that he was coming to her office with a status report.

"He doesn't remember the last two years, since the Wraith attack, Elizabeth. I'm really quite puzzled by this. He has symptoms of vertigo and headache, and of course, the amnesia." Carson Beckett sat down in the well-worn chair in front of Elizabeth's desk.

"I'm sure you're doing everything you can. He doesn't remember anything since the first Wraith attack?" Elizabeth was incredulous. So much had happened since that fateful attack. The SGC had finally been able to send reinforcements in the form of ships, supplies, and troops to assist them in the defense of the station. The Asgard were also a huge help in containing the Wraith after General Jack O'Neill had reminded them again how Earth helped them with their little 'replicator problem'. All Wraith survivors had been put into stasis until it could be determined what could be done with them. In the mean time, the Pegasus Galaxy had begun rebuilding, for the first time with the knowledge that the culling would finally be over. General O'Neill had decided not to continue as the head of the SGC despite some major reorganizations, had met with Elizabeth before retiring to determine next steps. O'Neill had strongly recommended that Elizabeth be allowed to remain in control of Atlantis. Colonel Sheppard remained on the station as had most of the original staff. Teyla Emmigan had decided to remain on the station as her people relocated back to their home planet. She continued on as a member of the SGA exploratory team and to act as her people's ambassador and advisor to Atlantis. A new leader had been appointed in her stead and she had felt freer to narrow her focus to her goals on the station.

Dr. Rodney McKay and Teyla stood restlessly outside of Elizabeth's office, waiting to be called in for an information update about the Colonel. "You really should be sitting down in your condition. Especially in light of what's going on. The less stress, the better." McKay's uncharacteristic display of concern touched Teyla. Rodney kept himself busy studying the huge caches of information and technology still being discovered on Atlantis and around the galaxy.

"Thank you for your concern, Doctor, but I feel fine. I am not too anxious to sit down." Her hand went protectively to her abdomen, over her growing baby. The door opened and Dr. Beckett stepped out with a look of worry across his features. "Can I see John now?"

"I wouldn't recommend it quite yet, lass. I think that we need to get him comfortable with the fact that he's not back at the time of the Wraith attack before we introduce the idea of your relationship and the impending addition to your family." He patted her stomach gently. "I'm sorry. I will call you as soon as his condition improves." He smiled lightly at her. "Rodney," the Doctor nodded his head at the scientist and strode back towards the infirmary. Rodney nodded back.

Teyla needed more information. "Dr. Weir, what do you think happened to John?" Elizabeth looked up at her.

"I wish I could tell you more, but I know as much as you do about the situation. The Doctor will keep us informed as to his progress. Perhaps you could check with your people and see if they ever had experienced this sort of phenomenon. Or maybe any of the other people you have encountered in your travels. Any information will help." Elizabeth stopped her fingers drumming on the desk as soon as she realized that she was doing it.

"I will, thank you, Dr. Weir." Teyla left with a purpose, at least. Something to divert her from the fact that her husband didn't remember anything about their life together.

Elizabeth organized her stacks of paper for the third time before she realized what she was doing. She didn't enjoy being distracted. She was glad at least that Teyla had something to do to keep her mind off things. Everyone on Atlantis had become such a close-knit family over the last few years that when any one of them was out of action, they all worried. She decided to put together some notes for her discussion with the General later on that day. She thought back to the beginning of this expedition and how Jon came to be part of it. Although Sheppard and General O'Neill didn't know each other very well, they had shared a kinship. They were more alike than either one of them ever wanted to admit. Both of them shared a strong connection to the Ancients. She had met the General briefly who had taken over from O'Neill, but he seemed receptive enough to her ideas and she felt comfortable he would support her in any actions that she felt were necessary.

"I'm sorry to hear about the Colonel's condition. Is there anything you need? Additional medical staff or supplies? I'd be happy to send Daniel Jackson your way and let him study some more Ancient artifacts, perhaps he could find something in the databases. He's been itching to spend more time on Atlantis anyway. I'll send him with the supply run that's coming through the 'Gate tomorrow." Colonel Carter's smile did a lot to cover for her concern, but not quite enough.

"How're the boys, Colonel? Are they 10 months old already?" Elizabeth decided to change the subject. Sam usually loved to talk about her kids, twin boys adopted with General O'Neill. They had been married last spring. "How's the General been?"

"Great, yes, it's amazing they're getting so big, and Jack's fine, too. The boys are keeping him busy. The kids are surprisingly challenging, considering the both of us survived the Go'auld for so long. How's the growing brood on your end? How many new ones do you have now?"

"Well, Lt. Commander Greene and Dr. Johnson had their first child, a girl, about three months ago. Several more additions to Teyla's people, but as there not here full-time, we sometimes forget how many they have now become. And Teyla herself, we expect her to give birth any time now… John had been so excited… He'll be fine soon, I'm sure. And in time for the birth of his child." Elizabeth looked down at her desk.

"We wish all of you the best. Please let us know if anything changes. I'll brief the General. Stargate Command, out." Sam said softly.

"Thanks, Sam." Elizabeth nodded to her. "Atlantis, out." The screen went blank and she heard the "whoosh" of the Gate event horizon blinking out. Elizabeth sat back in her chair and sighed. Nothing was ever easy in the Pegasus Galaxy.

John woke up again, this time feeling a lot more like himself. He sat up slowly, half expecting the vertigo to knock him back down. For now, anyway, it seemed to have subsided. He sat back against his pillows and surveyed the scene in the infirmary. Nothing out of the ordinary seemed to be going on, but things definitely looked and felt different. How or why he just didn't know just yet.

"Ah, Colonel, you're awake." Dr. Beckett came over to his bed and started to take John's blood pressure and pulse.

"Yeah, thanks.,..I did manage to wake up this time. What day is it?" John asked, trying to sound lighthearted, but knowing the answer probably wouldn't be what he wanted to hear.

"How about you tell me? What day is it exactly?" Carson stopped everything else he was doing and looked right at John.

"Where's Elizabeth? I want to talk to her." The set of his jaw showed that he meant business, at least that was the look he was going for. While the Doctor went to call Dr. Weir, John decided to get out of bed and make himself a little more professional looking. He peered into a nearby mirror and attempted to straighten his bed-head. _Not much luck there_. He couldn't meet Elizabeth looking like a mental patient, so he decided to head back to his quarters to change, maybe grab a shower. He tried to avoid as many people as possible to minimize the strange looks he was getting. He slipped into his quarters and headed for the bedroom. The décor was different from what he remembered, there were women's things around as well. _Had they reassigned his quarters to someone else while he was out of commission?_ _No_, he did notice some of his own stuff mixed in and a bunch of things he couldn't place at all. He sat on the bed, willing his head not to go all wonky_. How could all of this have happened? He couldn't remember the last two years? _He put his head in his hands and hoped for some inspiration.

"John? Are you okay?" He heard Teyla's gentle voice sometime later.

"Hmm?" He opened his eyes wider in shock as he saw her in entirety. "Teyla? _You're pregnant_?"

"Yes, John. The doctor says that I could have our…_the_ baby any time now." She smiled at him lightly.

"How did that happen? Well, I know how that happened…but who? Who's the father?" So many questions swirled around in his head.

"You are, John. We were married last year." She picked up a picture from the dresser showing the two of them smiling while cutting a cake, with everyone from the crew surrounding them. They looked unbelievably happy. She sat down next to him on the bed. "Do you remember anything from the last two years?"

"Nothing. To me, it's the day of the Wraith attack. I'm sure as hell glad that we all survived. I guess you'll have to fill me on the details about that and other things…" He smiled. "Do you mind?" He asked as he held his hand over her belly.

"Of course not, John. Please." She guided his hand to her stomach and placed it on her right side. "Here, the baby's been moving around a lot. If you wait just a minute, you may feel something…there. Did you feel that?"

"Wow, that's amazing! Do you know if it's a boy or a girl?" He asked as he moved his hand around her stomach.

"You said that you wanted it to be a surprise. Athosians never had the technology to determine gender before birth before, so I never considered it. What do you think?" She placed her hand on top of his.

"I think it's one of the best surprises you can get." He looked around again. "Do you know what happened to me the other day that may have caused this?" He turned to see her reaction when he heard his name being called over his comm.

"_Colonel Sheppard, this is Dr. Beckett. Please return to the infirmary. Your test results are in." _

He touched his comm, "This is Sheppard. Be right there….Teyla, do you want to come? My test results are back." He pulled on his uniform jacket and pants and ran another hand through his hair. "Do I look more presentable?"

"Of course, John." She tried to smooth out his hair again. She gave him a wry smile and gave up.

"Thanks, let's go." He followed her out into the hallway.

John, Teyla, and Drs. Weir, Beckett, and McKay all met in a conference room off of the main infirmary room.

"Okay, Colonel, some interesting things came up in your tests, but I'm afraid they may raise more questions than answers." Dr. Beckett queued up some statistics and charts onto a computer display set up near him. "I ran some diagnostic tests and compared the results to your baseline, which we had gathered when we all first arrived here. I didn't detect any substantial differences as you can see here," he pointed to some charts that didn't mean anything to John. The doctor described more data to the group that to John sounded like another language…. "Your ancient gene seems to have produced much more proteins that are circulating in your blood that we had ever detected in you before. I have compared some of your blood samples from when we first arrived to today and there is over a 400 increase in the proteins now."

"And what does that indicate, Doctor?" Elizabeth leaned forward in her chair.

"I'm not really sure. It doesn't seem to have too much of a physiological effect, except that his brain seems to be assimilating it a little more slowly than the rest of his body. Perhaps that is causing the headaches, the vertigo and the amnesia. I will run additional comparisons over the next few hours and days to see if there is any normalization going. We may have to do a spinal tap to determine protein levels in the cerebral fluid if things don't improve."

Colonel Sheppard sat back in his chair considering this possibility. It sounded just as preposterous as his amnesia. Teyla shook her head slightly, but showed no emotion at this news.

"Teyla, have you heard anything yet from your people?" Elizabeth asked Teyla, who seemed to be thinking very deeply about something.

"Um..I haven't heard back from Holling yet, there is a regional meeting he is attending. I expect to hear from him upon his return. I will report to you as soon as I can." Teyla reported, after regaining a little composure. She began to rise as Elizabeth adjourned the meeting.

"Doctor, please keep us informed. Thanks, everyone." Elizabeth's thoughts were still scattered as she left the room.

The soothing waves always seemed constant and ever changing at the same time. John sighed as he leaned over the railings just a little bit more. He came right out to the balcony after the meeting. Teyla had said something about needing to rest for awhile. He figured he should give her some room. The crisp wind blew right down the back of his jacket and he shivered. He tried very hard to think back to the last thing that made sense, back in the day of the first big Wraith attack on the station. _Nothing. _For once he was afraid that he would have to rely on his teammates to figure this mystery out. He was just too tired to think about it any more.

His thoughts did slide over to Teyla, he felt for her confusion over this whole situation. He had been committed to her and they were having a baby. _How could he not remember that?_ Not that he was against it, he wasn't, but it was awfully difficult to make the shift from being attracted to her during combat practice to having a family with her. He felt very disjointed with this whole thing. _How the hell was he going to get out of this? _

He didn't think about how long he had actually been out on the balcony until he began to shiver. Darkness had just started to fall and the last remaining beams of light from the sun stretched very far across the water. The warmth of the day had dissipated and the coolness of the ocean spread beneath him. He had a feeling of being very insignificant all of a sudden and realized how unusual that was for him. He rubbed his upper arms in an effort to warm himself and turned to leave.

Something like an echo formed in his head, "_We have a kill. We have a kill. One Wraith mother ship has been destroyed…" _A huge cheer swelled up from the group still gathered in the Control Room

"_Good news, Rodney…. What about the other two?"_ Elizabeth turned and faced John with a smile on his face. He did not return the sentiment as he knew what was coming. Elizabeth's face fell slightly at his lack of response.

"_Atlantis, the satellite has been destroyed_. _Grodin was on the satellite._ _The remaining Wraith ships are pulling back….Het's only bought us some time…." _

"_Understood, Rodney. Return to Atlantis…."_

"Sheppard? Are you okay?"

"Hmm?" The last voice was louder, more real. McKay stood next to him, John had not even noticed until he began speaking. "Yeah, I'm fine. Let's go in, I'm freezing." McKay followed him back into Atlantis.

John walked slowly back to his, no _his and Teyla's_ quarters, not sure if he really wanted to actually get there. The feeling of vertigo he had earlier swept back and made the edges of his vision fuzzy.

"_How many of you are in Atlantis? _

"_What's your name?…Okay, Bob it is. Tell..me…how…many..of..you …are in Atlantis?" He heard himself ask as he shot round after round into a hostile Wraith. _

He found himself staring at the door to his quarters, not quite sure what to do next. He breathed out slowly and willed his heart to stop pounding so fast. He knew, desperately knew, that something was wrong with him, with _everything_. He couldn't seem to figure it out and no one else seemed especially concerned with the fact that he couldn't remember anything of the last two years. He didn't even have any feeling of lost time, like the memories were locked away or something. There was just a blank, a hole. He sighed again and walked into his quarters.

People were concerned, several in fact. Elizabeth sat over a rapidly cooling cup of tea with Carson in the commissary, wondering what to do next. "I suppose we should request another military officer to fill in for the Colonel while he's recovering. Lt. Commander Greene would be a logical choice." Elizabeth was speaking, more trying to convince herself than the doctor that it was the right course of action. He nodded, knowing that she was not actually asking for his opinion on the matter. Those types of issues were what she usually discussed with the Colonel. She paused and swirled the tea leaves that had settled in the dregs at the bottom of her cup.

Carson pored over the sheaf of data that he had brought with him from the infirmary. He had run every test that he could think of, some several times. Nothing much out of the ordinary, besides the level of Ancient protein in his blood and his puzzling symptoms. The doctor and Elizabeth continued in their quiet contemplation of their problems for several more hours.

Carson's barely hidden yawn of exhaustion brought Elizabeth out of her thoughts. "You, to bed. I will see you in the morning." She rose from the table and followed him towards their respective quarters.

John lay next to Teyla, careful not to disturb her. Things were very distinctly weird. He stared at the ceiling in the darkness and wondered how the hell he was going to get out of this. He closed his eyes and let his thoughts wander.

"_Major, you stop killing my men and turn yourself in and I may not have to kill Dr. McKay here and the lovely Dr. Weir." John could almost see the grin of self-satisfaction on the face of the Genii General as he held Atlantis hostage. _

"_Never," he thought, as he ran through the station. "You will never take me alive. I will get us out of this." _The sound of a single gunshot ripped him out of sleep and sitting bolt upright in his quarters.

"John, it is alright. It was dream, you are safe." Teyla was rubbing his arm. He patted her hand as he tried to steady his breathing. All of this was happening for a reason. He just had to figure out why.

"I'm fine, Teyla. You go back to sleep. I'm going to take a walk. I'll be back in a little while. I'll have my comm. If you need me." He kissed the top of her head as he slid out of bed. He was amazed how natural it felt to have her here, caring about him. He pulled on a tee shirt and popped his comm. into his ear. He slipped into the hallway, almost in stealth mode, and he really wasn't sure why. He didn't see any reason why, but he couldn't shake the feeling that he needed to be careful. He stopped by one of the armories and convinced the guard that he needed to check something on a log or something. He grabbed a handgun and slipped it into the empty holster on his right side. _There_, now he felt a little more secure. _Can't be too complacent_. He acknowledged the guard and made his way down to the Gate room. He surveyed the darkened room and tried to convince himself that nothing was wrong. He had a little _niggling_ in the back of his mind, something… He took his gun out and kept it at the ready as he assessed the room. He walked up to the gate and touched it. The Gate began to activate, the chevrons locking into place with speed he had never seen before, especially here on Atlantis. The activation alarm sounded and several guards raced into the room.

"Colonel, drop the weapon! Sir, please drop the weapon!"

"Unauthorized gate activation! Unauthorized gate activation!"

John did not move until the horizon swooshed past him. He jumped through the Gate as soon as it stabilized.

"General, he's awake! Doctor!" John's eyes blinked open slowly as he saw a bright light being passed into his eyes. "Pupils equal and reactive. Pulse and respiration normal."

John blinked again and shuddered when he saw the face of General Jack O'Neill over his. "What the hell is going on,..sir?" He asked as he tried to sit up.

"I was hoping you'd tell us. You were requested to sit down in the Ancients' chair here after me and you went out like a light. You were out for a few minutes. How do you feel?" Dr. Beckett asked. The General looked at him in the most peculiar way.

"Where is _here_?" He looked around and saw Rodney, Carson, Dr. Jackson and a few others he remembered seeing only once before. They all were observing him strangely.

Dr. Jackson looked quizzically at John. "The Antarctica base, of course. We were hoping to find information about the location of Atlantis."

"Oh, crap."

9


	2. Chapter 2

**Part II:**

Major John Sheppard was entirely at a loss to explain how he had ended (began?) up back in Antarctica. Last he knew, he and his team had spent almost two years on Atlantis with no ZPM's to power a trip back to Earth. Now, here he was. And apparently, back where he started. _Had they heard of the Wraith? Did he still wake them up? Could he now stop it even before it started? _His head was swimming and laid his head back into the Ancient chair.

He blinked again and he was standing in the Gate room at Stargate Command. "Major, are you ready? You're the last one, sir, the gate's going to close soon. Pegasus Galaxy, here we come!" A young Lieutenant told him with much enthusiasm as he passed through the event horizon

John smiled and followed him through the shimmering pool of water to destination unknown, holding his P-90 at the ready.

"Major, can you hear me, please open your eyes…" Another light shone in his eyes. He blinked hard, his eyes tearing up slightly_. Okay, this is getting really old. Where, better yet, _when_ was he, anyway?_

"Yes, I can see that. Yes, I'm okay. No, I don't know what happened…" He started as he focused his eyes on Dr. Beckett. "What day is it?"

"Thursday, why?" Rodney answered from the next bed.

"What day, exactly?" John began to sit up as the Doctor took his blood pressure. The Doctor stopped as John finished his sentence.

"Don't you know?" Carson gave him the quizzical look that John was beginning to know quite well by now.

"I need to speak to Elizabeth."

"So you have been traveling back and forth in _time_?" Elizabeth sat back in her chair and observed the Major carefully. He had only list consciousness for a few minutes according to Ford and Teyla.

"So it seems. I was two years in the future, after the Wraith attack. We had eliminated the Wraith as a threat to the galaxy, Elizabeth. No more cullings. We had accomplished what the Ancients weren't able to. I'm not really sure of the details….I then found myself back in Antarctica, before any of this started, but before I could warn anyone, we were on our way through the Gate to Atlantis for the first time. Then I woke up again in the infirmary."

"Hmm…" Elizabeth stared at him.

"Look, I know that it sounds a little crazy. Here's crazy, I was promoted to Lt. Colonel, apparently on your recommendation." John sat back in his chair and watched the brain of Dr. Elizabeth Weir process the information.

"Yes, well. Report back to the infirmary and have the doctor make sure that everything's…right with you. Let me know if you have any more trips." She smiled and went back to her laptop.

"Elizabeth, you don't believe me?"

"John, if you were in my shoes, would you?" She gave him a concerned look and watched him as he left her office.

Maybe he was crazy, he had to admit that his story was completely out there, even to himself. He started to feel a little dizzy again and stopped short. _Aw crap, here we go again…_

"Sir, we've tried everything we could think of to get it off of you. Everything we had in the emergency kit. How are you doing, Major?" A very concerned Lt. Ford hovered in John's field of vision, which seemed to be fading ever so slightly as time passed and that _thing_ was still attached to his neck. He really wasn't in a lot of pain anymore; his legs and the tips of his fingers were now numb, like he'd been standing in very cold water for a long time. He decided that he wouldn't worry until he couldn't feel anything.

"Atlantis, we are not having any luck with the Major. Dr. McKay is still working on getting the engine pod to retract. Doctor, is there anything else we should try?" Lt. Ford spoke as calmly as he could, his eyes trained on the Major.

"Just work on keeping the Major hydrated and calm, we'll work on getting that thing off of him when you get back. " Dr. Beckett's worry was betrayed in his voice.

"Lieutenant, you have 12 minutes until the Gate shuts down. Please keep us informed." Dr. Weir's voice was eerily clam as John's hands gradually became numb. He felt as if he were slowly drowning. His thoughts were getting very sluggish and fuzzy. His throat was raw from screaming and he was getting to the point where he really didn't care what the hell happened to him with this freaking Wraith bug, he just wanted his people to be safe.

"Rodney?" John asked tentatively.

"Yes, Major?" Rodney with a tinge of annoyance.

"How are we doing with the engine…thing?" He forced out. The exertion to talk was draining him quickly.

"Dandy, just dandy. I'm working as fast as I can. You'll know the second I finish." He ripped another power bar out of its wrapper and chewed it hungrily as he focused back on the wrecked panel.

His brain felt so scrambled. He thought Teyla was sitting next to him, and as if to answer his question, she squeezed his hand. He felt only the slightest movement as the numbness was on the move towards his upper arms and lower abdomen. He smiled weakly and wondered if the future he had seen actually was going to happen or it all was just a crazy dream…

"Major, we have something we want to try. We think that the Wraith bug is somehow feeding off of you, if we stop feeding it, it should fall off…"

John just blinked slowly, trying to figure out what the hell Ford was proposing. "…use the defibrillator to stop you heart, just for a minute, pry that thing off of you, and then bring you back… Major?"

"Just do it."

He realized that the pain was gone, the numbness was gone, and he was free to move around. He was back in the Gate room in Atlantis, but no one else was around. He looked up and saw Elizabeth Weir working at a console. He watched as she worked on entering information and noticed that she looked older, somehow. Older than he had ever seen her, except when her double "woke" up from stasis…_Holy crap_… he was with her in the past, _way past_, when Elizabeth had agreed to keep the failsafe "safe" for when they would arrive on Atlantis, thousands of years later. His brain was reeling from all of this_, hell, he was no quantum physicist…_

"_John_."

He spun around to face whoever had addressed him.

"_John, I am called Veya. I am one of those you call the Ancients_."

He stood there, mouth open, unable to make himself respond.

"You are a descendant of my people, and as such, we were curious as to why you have come back here. When your heart stopped, it gave me a chance to speak with you in a way that you may not normally be open to. We are not actually here." She waved her hand around her and the environment shimmered into a blankness, nothingness.

"We are in a place between your world and mine, a very small place that rests between our planes of existence. I am only able to speak to you now because you are receptive."

"What, you mean _dead_?" He found his voice. He breathed out slowly and waited for her answer. He knew he would meet his end sooner rather than later, but never expected this. To be talking with an Ancient?

"In a manner of speaking. No one really is truly _dead_, your energy never dies; it is just _transformed_ into something else."

"John, I will offer you the chance to become more than you are right now, to know more than you ever could possibly imagine. Otherwise…" She spoke very carefully, as if it were a supreme challenge to communicate in the manner in which she was with him.

"Wait a _god-damned_ minute. Did you cause all this crap I've been going through? Why?" John's anger was beginning to rise, he could feel his blood pressure increasing with every word.

"We needed to make sure that you were worthy to be the Guardian of Atlantis. But, you could be so much more than that."

"I don't want to be more than that, I just want to go back. To the _right_ time! Do that for me and I'll forgive you for all of this madness."

"As you wish, John. We will speak again."

"Clear! Charge to 250. Clear!…Sinus rhythm has been established….Major, can you hear me?"

"Hmmm?" He had been run over by a truck, he was sure of it.

"Dr. Weir, Major Sheppard is awake." His awareness fuzzed out again.

"Major Sheppard, you are awake." Teyla set next to his bedside when he opened his eyes again.

"What happened?" He brain must have exploded, he was sure that there wasn't any way he could be in this much pain and still be alive.

"You're back." Elizabeth smiled at him.


	3. Chapter 3

**Part III:**

"I guess you could say that. Did you get that _bug_ off of me?"

"If you mean that _stunt_ was successful, then yes, it was. How do you feel?" John felt the chill of Elizabeth's words regarding what they had to go through to get the team and him back in one piece.

"Tired, but okay, I guess…." John opened his mouth to speak more, but then closed it. He thought that there was something else he was supposed to tell Elizabeth, but he couldn't remember what it was. He shook his head.

"Good, well, I'll let you get some rest and we'll debrief tomorrow 0900 hours. Goodnight, Major." She cocked her head and then started off towards the infirmary doors.

"Goodnight, Dr. Weir."

He awoke the next morning with the desperate feeling that he had forgotten to do something really important. He had a sinking feeling in his gut, but his mind couldn't find any reason for it. The doctor told him that he could be released to his quarters to recuperate and he thought that he actually would listen to medical advice and not overdo it.

"_He escaped." Beckett came running up to John and Elizabeth as they were planning what to do next to stave off the Wraith attack. _

"_Ford?" John asked, although he already knew the answer._

"_Yes, the guard didn't have a chance, Ford threatened all of us with the guard's gun. I think he's trying to get off Atlantis. He took all the Wraith serum we had left." Beckett's look of concern grounded John. _

"_I'll go get him." _

"_Be careful, Major. We don't have much time."_

He knew that it was a memory, at least it felt like one, but he was very, very sure that it hadn't happened. He shook his head in an effort to dispel the memory, _or whatever it was_, from his mind.

Dr. Beckett finally released him from the infirmary a few days later and he was raring to go back out there. He felt that if he didn't soon, he would never go through that Gate again. That whole thing with the bug and those crazy dreams or visions or whatever they were really put him on edge. He did not like being out of control of things, not at all.

"Major Sheppard." His comm. crackled to life in his ear.

"This is Sheppard." He hoped that they couldn't hear the uncertainty in his voice.

"Please report to the Control room, we have communication with the SGA team currently off-world."

"Roger that. I'll be right there." He actually was glad there was some sort of problem off-world. He needed to get involved again in the station. He just hoped it wasn't something that he couldn't handle. He grabbed the rest of his gear and started off towards the Control room.

He met Elizabeth in the Control room. She had a look of concern on her face as she tried to hear what the team was relaying. The reflections of the open Gate bounced off the walls in the Gate room, giving everyone in the room a strange blue tinge.

"_An entire Wraith fleet is approaching. Our shields will never withstand an attack of that proportion, Dr. Weir." A young officer now manning Lt. Grodin's chair told Elizabeth as she stood next to him viewing the same horrifying scans. _

"_We have to convince them that we are not here anymore…" Rodney began._

"Major, are you with us?" Elizabeth's voice brought John's attention back to the present, at least he hoped it was.

"Yeah…yes." He turned his attention to the off-world team. "Now what's the problem, Captain?" Elizabeth gave him a slightly confused look.

"We already covered that, Major. SGA-2 team is attempting to negotiate some food exchange for a small naquadah reactor to help power an emergency communications tower that was recently damaged in a storm." Elizabeth gently took the communicator away from him. She talked to him as she would to a child.

He nodded and kept quiet, looking intently at her to show that he was paying attention and desperately trying not to look guilty. "Capt. Fuller, you may proceed with negotiations. We will wait for news of your progress at the next check-in time. Atlantis, out."

"Yes, ma'am, SGA-2 out."

"Major, can I speak to you in my office?" Elizabeth requested, but John could tell that she was not really asking.

"Yes, Dr. Weir? Anything I can help you with?" He figured that a little levity might distract her form being annoyed at him as he looked across the desk at her. He was wrong.

"Are you okay, Major? You've been acting…strangely since… it's been awhile. Everything okay?" She put on what John considered her "concerned, I'm listening" expression. He sighed and sat down in the chair facing her.

"I guess I was, _am_, a little freaked out about the whole Wraith bug thing. I'll get over it."He decided right then not to bring up anything else; none of the little memory _flashes,_ where he checked out of reality for a little while, the intense feeling that he had to do something really important, or that fact that he thought that he spoke with an Ancient when he was dead. He had to deal with it on his own, do a little research or something._ They would send him back to Earth for sure… Wait, they had no way of contacting Earth right now. Where did that come from? _

He shook his head as he realized that Elizabeth was still talking and then quickly nodded in an attempt to look like he had been a participant in the conversation the whole time.

"…_if_ this negotiation goes well, we will be able to stock our stores for the next few months. We're not really sure if there are seasons here, but we need to be prepared for anything."

"Of course, Elizabeth. If there's nothing else, I need to do a security sweep." He stood up. He needed to get out of there. She shook her head and began typing on her laptop. He took as an okay to leave.

He strode out of Elizabeth's office and headed for the Control room. _It's not like he needed her permission to do his job or anything. Her acceptance would be nice…_ When he finally completed the sweep to his satisfaction, he made his way back toward his quarters and actually hesitated before opening the doors. What the hell did he think was going to be on the other side of the doors anyway? He flashed on a very pregnant Teyla standing there. He opened the doors with a swipe of his hand and darkness greeted him. His flipped on the lights and everything looked…_norma_l. Completely the same as he remembered. _Finally. _

He pulled off his uniform and slipped under unmade sheets of his bed and closed his eyes.

He was being shaken awake. "John? John! It's time. Wake up!" He blinked hard and looked into the flashing eyes of Teyla Emmigan.

"Time for what? What's going on?"

"The baby's coming. It's time!" He leapt out of bed after her and glanced at his clock. It read "0245" in red numbers. He thought that this had to be a dream. He wasn't _here_, really. He really was asleep in his bed on Atlantis, back in the right time. Well, he figured, he might as well play along. He may never get the chance to become a father again. Teyla leaned on him as they made their way to the infirmary after he made a somewhat frantic call to Carson. The doctor seemed to perk right up when he mentioned the reason that he was calling in the middle of the night. They stopped during fairly regular intervals for her to weather a contraction. John navigated her through every shortcut he knew through the station to get to the infirmary as quickly as possible.

"Teyla, how are you doing? Do you need to stop for a minute?" John asked as she paused again.

"No…we need to keep moving." She ground out. "The baby's coming very…fast. We need to get there soon."

He felt her shaking and the waves of heat that rolled off of her body. She was fighting very hard not to show the pain that she was feeling. He guessed it was for his sake. He prayed that the infirmary was at the next intersection. He couldn't stand to see her in so much pain.

They finally reached the infirmary and were met by several members of the medical staff. Drs. Weir and McKay stood off to the side, trying not to be in the way. John looked at them and they smiled back. He couldn't help but return their smile. All ideas that this was a dream left his conscious throughts.

Dr. Beckett and his team got Teyla set up for the birth and made a few checks. "She's just about ready, John. Teyla, you can push anytime you feel like it." She nodded silently and began pushing. She gripped John's hand tightly and he tried his best not to scream in protest. Carson's face lit up and he announced that the baby was crowning. "John, do you want to catch your baby?"

John looked at Teyla, whose face bore the signs of exhaustion and sweat, but happiness as well. She smiled and nodded. He let go of her hand and moved down by where Carson was stationed. The nurses slid a surgical gown over him and Carson moved out of the way, but remained next to him. Elizabeth and Rodney had moved by the head of the bed and were holding Teyla's hands. "One more push should do it, lass." Carson said gently. "Now, John, place your hands here. The baby will come right out with this next contraction." With a gush, Teyla cried out and the baby fell into John's outstretched arms. He was speechless and motionless until the baby began to move. "Okay, let me clamp the cord. Then the babe will cry." Carson moved to take the baby away from John for a few moments.

"What is it?" Rodney asked excitedly. John hadn't even thought about it. He was too relieved that everything went fine. Carson placed the baby on Teyla's stomach when he was finished.

"It's a boy." John answered, Teyla smiled deeply and stroked her newborn. His son chose that moment to let out a hearty cry. He and Teyla laughed out loud in response.

"Congratulations!" Rodney smacked John on the back and Elizabeth hugged him. He couldn't stop smiling.

"Major Sheppard! Major Sheppard, please report to the Control room. We have an unscheduled activation!" His heart was pounding as he sat up in his bed. His arms ached with the absence of his son. His ears still rang with the baby's last cry.

"Major Sheppard, do you read?" He heard over his comm. link.

"This is Sheppard. I'll be right there."

He pulled on his pants, stepped into his boots, and ran down to the Control room.


	4. Chapter 4

**Part IV:**

He immediately crouched down in response to weapons fire that was coming out of the open wormhole. "What's going on?" He yelled up to the Control Room.

"We received the IDC of Major Lorne's team, sir. Shall I put back up the shield?" A nervous voice came over John's comm.

"No, Lieutenant,…wait…give them one more minute." He dodged three more close calls and hid behind some containers while the team flew through the gate and crashed onto the ramp in front of the shimmering pool. He counted the four members of Major Lorne's team.

"Raise the shield!" He screamed as he ran towards the prone team. The shield came on and several hits were heard before the 'Gate disengaged. "Get Medical down here!" He felt the Major's neck for a carotid pulse and let out a breath when he felt one. The rest of the team seemed to be in various stages of attempting to get up.

"Everyone stay where you are. Medical's on their way. We'll debrief in a few hours." He told them gently. They nodded in response and let Dr. Beckett's team help them onto gurneys. John followed the Major's gurney, hoping to get some indication of what had happened. He shook his head as Beckett and his team rushed them into the infirmary.

Dr. Beckett seemed to read his thoughts, "I'll let you know when they're up for visitors." John nodded and left. He watched the infirmary doors close as he stepped backwards into the hallway. He then noticed how quiet everything had become and deserted. He headed over to Dr. Weir's office to debrief her on the little that he did know about the situation with Major Lorne's team. He couldn't remember what mission they were even on. He didn't recall giving permission or even going over mission specs for a potential off-world exploration for Maj. Lorne as far back as a few weeks ago. _Oh, man. Elizabeth was going to flip out. _

He knocked on the door to Elizabeth's office before he entered. "Come in." He heard and complied.

"Colonel, is your team ready to disembark?" He was about to protest when he noticed that he was now wearing his mission gear and holding his P-90. "Good luck." He continued to stand in stunned silence, feeling a little fuzzy around the edges, and desperately hoping that his memory would miraculously return to him. "Is there anything else I can help you with, Colonel?" Elizabeth looked at him quizzically.

"Yeah, where are we supposed to be going?"

"…And you don't remember anything about how you got to be standing in Elizabeth's office?" Dr. Beckett asked him for the third time as he shined a light into John's tired eyes.

"No…I..don't." He was really getting sick and tired of explaining this to everyone, whatever the time. "Look, I'm sorry, but I've explained this to you a whole bunch of times and I'm starting to get tired of the plot." John sighed and slumped down on the exam room bed.

"Don't worry, Colonel, we'll figure this out. All we have so far is that a certain protein biomarker is in a higher concentration than normal. That's seen in all the people on the station who have the Ancient genes naturally. I haven't seen any complications from it. Call out if you need anything. Try to get some rest. I'll check on you in a wee bit." He patted John on the shoulder and left him alone.

He slid all the way down so that his head was now resting on the flimsy pillow that was standard in the infirmary. He suddenly felt as though he hadn't slept in years and fell into a deep sleep.

"Ja-ahn…. John, wake up." Her sing-song voice woke him up.

He opened his eyes and saw that Veya was standing over him. "Uhhh, what are _you_ doing here?"

"John, I told you that we would meet again. Are you ready to talk to me now? With a little more decorum this time?"

He slung his arm over his eyes in hopes that she was just a dream. He waited a minute and then peeked out and saw her still standing there.

"Alright, I give up. Am I dead again or what?"

"You're the same as you always were, John. Do you understand _now_ why you've been experiencing all of this?" She looked at him closely.

He sat up and looked into her eyes. "No, I can honestly say that I have no idea what the hell is going on. Why don't you enlighten me? Isn't that what you _do_?"

"Oh my, John. Why must you be so troublesome? You humans always did have a stubborn streak. Look, Atlantis is not just a station, not just repository of our knowledge, it's a sort of gateway to our plane of existence. You and your group did not come here by accident. Everything you've had to go through is part of a test, to see if you're worthy."

"Worthy of what? Worthy of being thoroughly pissed off? Because we're rapidly approaching this threshold. Wait..there…now we're over it. Let's cut to the chase, shall we? What do you want from me?" He was barely containing his rage over her arrogance.

"We have decided that we will let you have access to all the secrets of Atlantis. You have made amazing progress in dealing with the Wraith. We are very impressed. However, you still have a long way to go before you can ascend to our level. We will be watching, but you will also need to be watchful. Many challenges still await you. Good luck to you and your people, Colonel."

"Wait…wait!" John screamed after her when his surroundings seemed to fade away.

John woke up in his bed, in his quarters, alone. He looked around and noticed that everything looked pretty normal, like it was supposed to, like before all of _this_ happened. He sighed. _Thank god, thank the Ancients, whoever. _He thought about what he did yesterday and it seemed to be all there. His memory seemed to have recovered from all of the "holes" that he felt before. He remembered being promoted to Colonel and he remembered their narrow escape from the Wraith hiveships. He wasn't really sure if _this, here, today,_ was real, but he really wasn't in the mood to second-guess right now. He decided that he was going to act as if everything was fine and therefore he _would be_ fine. He knew that there were flaws in that logic, but he didn't care anymore. He was in too good of a mood. He got ready in preparation for the day. He was smiling, even whistling while he walked to the mess hall. He was getting strange looks but he didn't care. Everything was back to normal. He wanted to write the whole thing off to a bad dream, _a really long, really vivid bad dream_.

He grabbed some breakfast from the mess and settled on one of the nearest chairs where Rodney happened to be sitting. "Rodney." John acknowledged.

"Colonel."

"Anything interesting on tap today?"

"Hmm?…Not really, nothing more than usual. We're set to map more of the lower levels. You're still coming, right?" Rodney told him between bites of his bran muffin. "Teyla and Ronon will be leading teams to search the North end and you and I will be leading teams to start on the South end….If you're still coming, of course.

"Why wouldn't I go? Sounds like fun. I need to talk to Elizabeth and make sure there's nothing else that needs my attention, but otherwise, we're on. What time?" He happily dug into his cereal.

"0830, your time. 8:30 am, my time." Rodney practically snorted with that one. John smirked and finished his meal.

"See you in a bit, Rodney, and make sure that you eat up. I don't want you fainting from hunger again."

"I don't faint, I may _collapse_, but I never faint." He gulped down the rest of his orange juice.

"Uh huh, sure you don't." John nodded and jogged off to see Elizabeth. He was brimming with energy, he felt so good, so back in control.

Elizabeth was surprised to see him in such a good mood. It had been a really long time. She actually felt a little uplifted herself, reflecting his good spirits. "What can I do for you, Colonel?"

"Nothing, unless you need me for something. Rodney and a few of us are going exploring in some of the lower tiers. Should be back before evening chow. It's tacos tonight." He was positively brimming with energy now.

"Great, have fun." She smiled as he trotted out of her office and headed towards the supply room.

(Please review…any suggestions would be most appreciated! Thanks to everyone who has written already.)


	5. Chapter 5

**Part V: **

_A/N: To all who have reviewed so far, thanks for reviewing and don't worry, all will be explained. Thanks for sticking with this story so long! And for the orange juice that Rodney drank in the last episode, please excuse my momentary lapse in consideration for poor Rodney's citrus allergy, it won't happen again! _

John and one of the scientists, Dr. Brian Ferdinand, a nuclear physicist by training who had just arrived with the last run of the _Daedalus_, were searching one of the lower levels when his mind began wandering. Nothing was really going on, the scientist was waving some piece of equipment around, looking for energy fluctuations or something. He was really only there to make sure that the scientist was safe to do his thing. He kept thinking about what Veya had said to him, that all the things that he had to go through were a test of some kind. He didn't really see how everything was related, his bouncing around in Atlantis history and future, seeing possible futures with him and Teyla, and meeting an Ancient _with an agenda_. _They all seemed to have an agenda didn't they?_ No one else seemed to remember him having any issues with the future or the past or even having had complained about it and it was going to stay that way. He didn't need Elizabeth and Carson looking at him the way that he had seen so many times after his _episodes_. He wanted to discuss this with someone desperately to help him make sense of it, but he didn't need any of the complications. He immediately thought of Teyla, who might understand his need for discretion and may be able to give him some insight. He needed to consider what to tell her, though, if he should mention that whole _married with a child thing_. He could just see her reaction now, she would smirk a little and raise her eyebrow, almost Mr. Spock-like. And she wouldn't comment on it at all. Well, maybe he would leave that part out for awhile and tell her the rest and see how it went.

"Colonel! Colonel Sheppard, come in!" He was interrupted in his musings by a really excited transmission from Rodney.

"Sheppard here. What is it, Rodney? Find something?" He just knew that McKay would find something that would make him squeal like a child in a candy store, he always did.

"Find something? _Find something?_ Hell, yes, we found something. Another Ancient chair. Get down here, I want you to try it!" Rodney was practically screaming into John's earpiece now. John glanced at Dr. Ferdinand who was wincing at the volume of McKay's outburst.

"Okay, okay, McKay. We'll be there in about fifteen minutes, we're at the other end of the complex. Sheppard, out."

"C'mon, Ferdinand. We have some Ancient furniture to check out." He had a bit of a strange feeling about this, but shrugged it off as typical McKay enthusiasm about all things Ancient.

By the time John made it over to Rodney's team, most of the others had already congregated around the chair. They all parted when John arrived, except for some of the newbies. They had never seen what John could do with a little Ancient technology. He laid his P-90 against the side of the chair platform and sat gingerly down in the seat. He closed his eyes and…waited.

"Colonel, could you at least try to activate it!" Rodney yelled in his exasperated tone.

"I am, McKay! Do you think that I'm sitting here for my health?" John spoke from between clenched teeth. He had been taking his ability to work the Ancient stuff for granted and was genuinely surprised when it didn't work. "Does it have power?"

"According to the readings, it is being supplied off of one of the ZPM's we have. It may just take some time to get warmed up or something. Try thinking about activating it again." Rodney's voice seemed to have ratcheted down a few more notches, as he focused on the output from his laptop set up nearby.

John leaned back into the chair and closed his yet again. The lights in the room dimmed as the chair powered up. A collective gasp was heard as the ceiling was filled with a star map of the Pegasus galaxy swirling in a slow clockwise direction. John opened his eyes slowly, "How's that, McKay?"

"Good, good. Can you make it do anything else?"

"I don't know. What do you want me to ask it to do?" He closed his eyes again and opened his awareness to whatever the chair wanted to tell him.

"_John, what name have you selected for our son?" Teyla looked at him with exhaustion and pride as she held their son out to him. He pulled his son back into his arms gingerly._

"_Max, after my brother. I don't know if the universe is ready for another Sheppard." He laughed as Teyla nodded at his selection. He gave her back the baby and thought that he couldn't possibly be any happier. _

"_It is a strong name. My people will also be pleased." Teyla said softly to John. _

_Then they all heard the klaxon. "Unscheduled activation! Dr. Weir and Colonel Sheppard to the 'Gate room." John heard over his earpiece. He glanced at Teyla who mouthed "go!" He leaned over and kissed her and their son as he and most of the people in the room raced to the 'Gate room. _

_John already knew what was going on before they got there. The Wraith had just figured out that they still existed. Atlantis would fall this time._

"Colonel? Are you okay?" McKay's face loomed in front of his as he opened his eyes. Drs. Beckett and Weir were standing behind him.

"Why, what happened?" He sat back up. No one else was left in the room, and the lights had come back on but still seemed dimmer than he thought they were before. His head was pounding and he had the suspicion that he may have been out of it for a little while. Especially since Beckett was there. Speak of the devil…Beckett shined his ubiquitous white light into John's eyes, which made him blink furiously. He swiped the Doctor's hand of his face as he tried to get up.

"Now, Colonel, please remain seated until I compete my exam." Beckett grabbed his wrist in order to take his pulse.

"What happened, McKay? How long was I out?" He saw from Rodney's expression that neither would have a good answer.

"You sat down, no, you remember that, don't you? Well, after that the lights went out all together, no star chart, no nothing. The whole chair assembly began to glow and you started speaking, in Ancient, at least it sounded like Ancient, but it was so quiet that it was hard to tell. You may have just been having a seizure or something, so naturally I called Carson and Elizabeth. By the time they got down here, you were starting to come around and you just woke up. Do you remember anything? Did anything happen to you?" Rodney was rambling, a sure sign that he had actually been scared of what was going on. And that made John nervous.

"Umm, nothing that made any sense. Doc, am I free to go?" He pulled away from the Doctor's ministrations and slid off the chair.

"Your vitals are normal. Do you have any dizziness, any pain, headache?" The doctor asked as he reviewed his data pad.

John shook his head in answer to each question, "I feel fine, I'll let you know if anything changes. Thanks and sorry for all the trouble." His head was buzzing from everything, but he didn't want Beckett to get concerned. He waved everyone off as he strode out of the room.

This was now hurtling past annoying, right past ridiculous, and storming right into "this had to stop"_. Now_. He needed quiet for a little while to think about what to do. His earlier good mood was definitely gone. He made his way back up to the transporter and thought his way to one of the lesser-traveled upper tiers. The sun had just set and the breeze blew gently across his face as he stepped onto the closest balcony. He really didn't know how to handle this, here a soldier, faced with a challenge, and he had absolutely no idea how to proceed. He knew that he would have to tell Elizabeth and eventually Carson about this and it would most likely get him grounded and perhaps put on restriction to the infirmary, or even some sessions with Heightmeyer. _Joy. Perfection. The Ancients were wondrous indeed_. He snorted to no one in particular. He fought the sudden irrational urge to jump over the side and into the ocean, when something caught his attention.

"_We want the one who flew the Dart, are you the one?"_

"_I flew the ship. Take me." Sheppard stood out from his group to the Wraith who was asking. _

_Sheppard was forcibly pulled from the cell and stole a glance at Teyla before they dragged him out. He presumed to his death. _

"_If he dies, you die." Ronon threatened Ford just before John was pulled out of earshot. This would be the last time he would ever see his team again. _

He rubbed his arms where he swore he could still feel their cold hands gripping him. He felt a deep sadness inside as he knew that that memory or vision or whatever _would_ come true. His eyes swept the darkened sea with new eyes, knowing that his time here was limited. He had to do whatever it took to keep Atlantis safe.

"John, are you unwell?" Teyla's soft voice broke him from his thoughts some time later. He hadn't realized that it had gotten so late because he had been so wrapped up in his thoughts.

"No, I'm fine. Are you okay?" He asked gently, sweeping her forehead with his fingers to move a piece of hair from her eyes. She looked right into his eyes and considered him for a moment.

"I am fine. I have had the feeling that you needed to speak with me, about something of great importance. Is this true?" She was close enough to him that he could feel her breath on his face.

"I'm not really sure where to start. Things have been happening to me…things that are very hard to explain and even harder for me to understand. I haven't told anyone, even you, because of what it could mean…frankly, it scares the shit out of me. " He turned back towards the ocean.

"Sometimes sharing the burden helps to lighten the load on one's soul. Please, I will listen. If I can help, I will. If not, you will not have to carry this all yourself. Come, let us return inside out of the wind." Her arm wrapped around his shoulder deftly guided him back into the observation room.

They spent the remainder of the night discussing John's experiences and what it could mean for himsepf and Atlantis. He decided that he would tell her everything and let her decide what to take out of it.

"A baby, a boy?" She asked quietly. She smiled that knowing smile that he knew he would see when he told her about their son. "I would not mind that future, John. You are well-suited to be a father."

"You think so?" An upwelling of pride surged within him, surprising him a little bit. "Thanks, I appreciate that. Even if it was all a dream, it was a really good dream, while it lasted. You would make a great mother."

"Thank you, John." She sighed and moved closer to him on the bench on which they were sitting. "Why do you this is happening to you?"

"To tell you the truth, I really have no idea. I know it has something to do with this damned Ancient gene that everyone seems so hot to talk about all the _damn_ time, because that's a theme that seems to be running through all of this." _God, she was so beautiful_. His thoughts wandered away from the topic and he wondered what it would feel like to kiss her again. Not under the influence of anything.

"…perhaps Dr. Weir or Dr. McKay may be able to help you sort this out. There may be something in the Ancient database that would explain your experience." He had to refocus on what she was saying.

"That's a good idea. It's getting late, maybe we should be getting back." He stood up slowly, not quite wanting his time with Teyla to end. He remembered his "time" with her as her husband and thought about how natural it felt, so easy. _Why had he never seriously considered it before? _

He had dropped Teyla off at her quarters on the way to his own, knowing full well that he wouldn't be able to sleep tonight, _no, scratch that_, the remainder of the dawn. He sat at the window in his quarters just watching the sun slip above the horizon, its beams of light spreading over the surface of the fairly calm waters. Waters that had covered up so much death and destruction. He sometimes felt like that, calm on the surface to everyone else; but underneath, churning with all the guilt and knowledge of what he had done since he had been here. Was all of this a test? He wished that he could understand. He leaned on the window ledge and did not realize that his eyes had closed in response to his exhaustion.

_He felt himself being dragged again, by those cold, dead hands of the Wraith, dragging him to the end of everything. He opened his eyes slowly to see the halls passing by, additional Wraith joining the procession to wherever the hell they were taking him. They wanted information…how could he fly the Wraith dart, where was his homeworld, how could they get there? He could almost hear those thoughts flying between them. Teyla must be going crazy being stuck here on the Wraith hiveship, hearing and feeling everything those things did._

"_What is the address to your homeworld, human? You will show us." To emphasize their point, one of them placed a hand on his now exposed chest and extracted just enough energy to make him scream. _

_He would not….ever…tell them. He knew that Ronon, Teyla, and even Ford would never betray Earth to these monsters, but Rodney…he wasn't a soldier, would he be able to withstand torture and hold out until they killed him, too?_

_They continued his torture for what felt like years when they finally stopped and dropped him in a boneless heap in the middle of the room. He felt his life slipping slowly away and he couldn't do a damn thing to stop them. He felt a hand on his shoulder._

"John. Open your eyes."

He was now looking into the form of Veya again, this time resplendent in long, white robes and she was _glowing_. "John, it's time for you to decide."

"Is this real? Is this really happening?" He looked into her eyes and searched for an answer that he wasn't too sure that he wanted to know.

"John, _this is happening. This is real_. As much as anything is. Everything you've been experiencing has been your mind's way of determining if you think you are worthy to ascend. It is time, John, to make your decision." She pulled him to his feet and he felt completely fine. His uniform was intact and no one else was in the room. Just him and the glowy Ancient. _Oh shit._

"What? My decision. My decision is I can't leave my team to die. I can't leave Atlantis vulnerable to the Wraith. Remember those bastards, the ones that even the great Ancients couldn't eliminate?" He stood defiantly in front of her.

"John, you still don't understand, you don't have a choice in that. Whatever happens to Atlantis and your people is out of your hands. Your choice is to ascend or to die. Atlantis will survive as it is supposed to, because of what you've already done to save them."

"What the hell kind of answer is that?" He restrained himself from grabbing her shoulder and shaking them as hard as he could. "How can I leave when the greatest threat to you and humanity is still out there?"

"It is the truth and you must. Events that have taken place have done so because the universe has supported it. They could not have occurred any other way. You must understand that by now. Even _we_ cannot change the way of things, but we can fathom their purpose. Please John, I am here to help you in this transition. I have been trying to help you for some time. You need to realize that you cannot influence events from your past life any longer. You only have one things left to do, ascend or perish. If you ascend, you will have the ability to participate more fully in the workings of the universe, but you will be forbidden from interfering with the actions of your past life. If you choose death, your spirit will be released and will travel to wherever it wants to go, but no consciousness will be retained. What is your choice?"


	6. Chapter 6

**A/N: Short update, Part VII in progress, will post as soon as possible. Happy Holidays everyone!**

**Part VI:**

"Colonel, what is your choice? Would you like to stay in the village and conduct the negotiations or travel with Dr. McKay and his group to the ruins in the west?" Teyla looked at him quizzically. She and the remainder of SGA-1 standing behind her waited for his response. Native people stood near their group, seemingly awaiting instructions on how he would like to proceed.

"Uh, what…whatever you want is fine…" he stuttered as she continued to look at him with a puzzled look on her face, "…or I could escort Rodney and the research team. We'll be back by nightfall."

She smiled and nodded slightly in response and turned to speak with one of the native leaders. "C'mon, Colonel, daylight's wasting." McKay chided John. John followed McKay and three other scientists towards the site of the ruins. _This was getting really old, really fast_.

They trudged onto where John assumed there was ruins, or something, hoping desperately that someone in the group had some clue as to why they were going there. He couldn't seem to recall any specs about this mission and of course, that seemed to be happening more often than not. He couldn't seem to stop it even if he wanted to ground himself from missions, so he just kept walking. He continuously scanned the horizon, following the group towards something that seemed to be arising out of the edge of a wooded area.

McKay and others were chattering about something they expected to find, something on one of their damned scanners or something. John didn't know or care at that moment. All he wanted to do was get back Atlantis and crash into his own bed. He felt as if he hadn't slept in years. He realized just then that the group had stopped moving and he was able to prevent himself from crashing into McKay only by an inch or so. He backed up quickly and hoped that Rodney hadn't noticed.

"Colonel, do you mind? A little personal space would be nice." _Of course not, McKay never missed anything. _

"Uh, sorry. I was looking at the ruins. What do you think they are?" He tried to cover quickly. Asking Rodney for his opinion on anything was usually a great way to distract him from anything else that was going on.

"Well…" Rodney began his diatribe to explain what he perceived the ruins were and how they came to be in their current state. The other scientists listened with rapt attention. John didn't hear any more than the first word.

"Colonel, can you hear me? There's been an accident…" John became fuzzily aware that he was no longer vertical. Dr. Beckett's blasted penlight was being shined in his eyes.

"What?…What are you talking about?" He began to sit up, but thought better of it as his head began to swim. He felt a hand gently pushing him back into the bed. "Did something happen at the ruins?"

"I'm not really sure to what you're referring. You were exposed to something on planet PXR-345 and you collapsed just as you came back through the Gate. The rest of your team seems to be unaffected. You were involved in negotiations to increase our fresh food stores. You've been in and out of consciousness for two days." Elizabeth leaned in next to Beckett. "How do you feel, John?"

He took a quick assessment. "I'm good." _Two days?_ "Can I go now?"

"No, you cannot. You were exposed to something off-world and I can't have you traipsing around Atlantis spreading it around, especially if you've been unresponsive for the better part of two days. You also have symptoms similar to ones I've seen in people with allergic reactions. We need to complete our analyses first. Now just lay back. The nurse will be by soon to take your vitals. Elizabeth." Carson nodded as he strode away to talk with members of the medical team.

"Carson." Elizabeth acknowledged. "Now John, do you remember anything about what happened on that planet? Teyla said that you had gone with the High Councilor to discuss things in private. You had been separated from the group for about an hour or so. What did you talk to him about?" Her eyes seemed to be boring holes into his own.

"Uh, actually, I have no recollection of anything that happened on that planet. The last thing I remember is tramping after Rodney and some scientists to look at some ruins or something. What the hell happened? Exposed to what?"

"Dr. Beckett said you seemed to have some sort of allergic reaction to something. You had passed out when your airway swelled shut. They had to give you epinephrine to keep you breathing. You don't remember any of this?" She pulled up a chair and sat next to the head of his bed.

He shook his head slowly. "Nope, nothing. What did the tests show?" His patience was pretty much gone now. He figured that he might as well get more information; it may come in handy in his next "jump" somewhere else.

"Carson seems to think it's some sort of synthetic compound, your blood tests showed that your body was unable to properly respond to it as it would to an organic infection."

"Do you know if there was any significant increase in unusual protein levels?"

"I'm not sure, Carson's still running tests. Why do you ask?"

"Oh, no reason, I thought I heard someone say something like that. I'm pretty tired now, do you mind if I get a little shut-eye?" He flashed her one of his smiles, hoping she would acquiesce.

Elizabeth nodded and smiled. "Sure, I'll stop back in a little while. I hope you feel better soon."

"Thanks." He closed his eyes and feigned sleep. He was royally sick of all of this "jumping". He always seemed to end up here in the infirmary though. Hmm… He must have really fallen asleep because the next thing that he was aware of was being shaken awake.

"Colonel? Good morning. Time for your vitals check." As a nurse was taking his pulse, he noticed that Carson seemed to be deep in though staring at his laptop set up on a workstation. Carson's face then became blank, as if he switched off a light switch and started to come over to his bedside. _Probably didn't want me to get worried. _

"Good morning, John. How are you feeling?" Elizabeth seemed to be forcing a little bit of perkiness into her voice as she arrived from the doorway.

"I'm good. What did Dr. Beckett say?" He tried in vain to sit up, but the entire room spinning put a quick stop to that. He swallowed, hoping that he could keep the nausea down.

"Why don't you let him tell you? I'll check back in a little while. Feel better, Colonel." Elizabeth smiled, the enigmatic smile she always sported when things were unsure. He swallowed again.

"Ah, Colonel. Good morning. How do you feel?" Carson's demeanor, almost chipper, set John's teeth on edge. _What the hell was going on anyway?_

"You tell me, Doc. What's my situation?" John asked in a carefully neutral voice.

"I'm concerned about your lapses of consciousness and your memory loss. Your temperature is slightly elevated, but not in a danger zone. Could be a reaction to whatever you were exposed to. The agent seems to have been non-persistent, as we found no trace of anything out of the ordinary in your work-ups. We did have one curious finding though…"

"Let me guess_, elevated protein levels of an unknown etiology_."

Carson's mouth fell open at John's statement. John had only heard about it five times already. He wasn't fully sure what it meant, but he was at least consistent. "How did you know?" Carson asked incredulously.

"I..uh..I've heard this before. Several times in fact." John stared past the doctor. He didn't want to have to get into this again. _It hadn't helped in the last few times_.

"I think that you will have to elaborate on that, Colonel."

"I figured you would say that." John sighed.

Twenty minutes later, Drs. Weir, Beckett, McKay, Zelenka, and Heightmeyer were gathered around his bedside as he recounted his experiences over what he could figure spanned at least several years.

"Colonel, that is an amazing experience. I have to tell you, you've been here in body and mind continuously as much as we can tell all the way up until you passed out from your visit to PXR-345." Elizabeth said gently. "Are you telling us that you think that you've been experiencing time travel with the possible help of an Ancient?"

"Yes, I guess that's what I'm saying. I know that this sounds crazy; you've all had this same reaction many times before. Elizabeth's sent me to you, Dr. Heightmeyer, several times in fact. I really don't have any logical explanation for all of this. Now, tell me what year this is. What's the situation with the Wraith? That should help get me my bearings."

Everyone in the assembled group looked at each other uneasily. "It's 2006, January, Earth time. The Wraith has been quiet for the time being. Rodney devised a way of making it look like Atlantis had been destroyed. Do you remember that?" Elizabeth answered.

"Yes, I remember that. I'm glad to hear it." He smiled. _Finally, he was back where he was supposed to be._ "This is the time that I'm supposed to be in right now. Is Ronon here? On Atlantis, I mean?"

"Ronon, sir?" Lt. Aidan Ford stepped towards his CO's bedside. John's heart sped up in hearing his voice.

"Ford, what are you doing here? Are you okay?" He sputtered, mostly out of surprise in seeing his subordinate, alive and well.

"Yes, sir, I'm fine. Where else should I be, sir?" John slumped back down in his bed. _This wasn't right._ Ford was supposed to be off somewhere after being changed by the Wraith and they had found Ronon on the run from the Wraith_. Not that he wasn't glad to see him, that he was safe. _

"Uh, nowhere, here. Glad to see you, Ford. Has the Daedalus been here lately? Colonel Caldwell?"

"The Daedalus was destroyed two months after we returned from Earth. All aboard were lost. Some sort of malfunction in the Star Drive. We are cut off from Earth until the Daedalus II is completed, in about six months." John shook his head in despair. _How the hell did all of this change? What changed? Did he do something to make everything different? This was different than before. The present was different, instead of the future. _

"Okay, everyone, give the Colonel some time to rest. You can speak with him again in the morning." Dr. Beckett shooed everyone out of the infirmary. "Let me know if you need anything. Try to get some rest, we can make sense of all of this in the morning.." He patted John on the shoulder gently before he stepped out of the area and back towards his private office.

John smiled weakly. "Thanks, Doc." He knew that everyone thought he was crazy again, just like before. He had to find out something concrete that he could use to figure this whole thing out.


	7. Chapter 7

**Part VII: **

**(A/N: All medical references have little if any basis in actual medical fact. I'm not a doctor.)**

Rodney was working in his lab on some devices that he was in the process of taking apart and was thinking about what John had said in the infirmary. He seemed to be under the delusion that he was time-traveling with an Ancient or some other such nonsense. He really_, really_ wanted to dismiss it as some figment of the Colonel's imagination. He couldn't _quite_ do that. He thought about all the artifacts and databases with the Ancient information that they had discovered in their time on Atlantis, all the things that seemed impossible, but _were_ possible. He grudgingly admitted, _only to himself_, that the Ancients were very advanced and it would be some time still before he understood everything that they had found. He put the device down and leaned back in his chair. _What if John was telling the truth? _

John woke up again and smiled slightly when he realized that he was still in the infirmary. _Well, that was a first. _It meant that he hadn't jumped anywhere and he didn't have any visits from a certain Ancient woman. He strongly considered feigning sleep again when he heard Rodney calling to him.

"Colonel? John, you awake?" Rodney poked his head around the curtain that he been partially pulled around John's bed.

"Yeah, Rodney. What do you want?" It came out with a little harder than he meant. He was really frustrated at his situation, not Rodney. He had to be more careful that he didn't take it out on the easy target that Rodney was.

"Uh…well…I wanted to say that what you said _might_ be possible, considering everything we know, and don't know, about the Ancients. We know that they did have time-travel capabilities. We know that you are especially sensitive, shall we say, to the Ancient technology, being distantly related and everything. So, logically speaking, it just _may_ be possible for all of this to happen. I just wanted to tell you that." Rodney turned as if he was going to leave.

"Wait, Rodney." John grabbed his arm. "Thanks, I appreciate that. I'm glad that not everyone thinks I've cracked."

"Well, I didn't say _that_." Rodney smirked and started to leave. "Let me do a little research, see if there is any reference to this type of thing in the Ancient databases. Okay?"

"Thanks, Rodney, I appreciate it. I need to talk to Carson to see about getting sprung from here. I'll catch up with you later." John felt a renewed sense of purpose. Maybe he wasn't just crazy after all.

Elizabeth stood at the railing overseeing the Gate room visualizing John and his team returning from some mission, all in good spirits. She imagined hearing him laugh about something that Rodney said at a negotiation. Teyla following, hear head turned to talk to Aiden. Rodney stumbling behind, managing to catch himself from tripping as he came through the Stargate, even after as many times as he's gone through. She smiled, wishing that every time they went through the Gate they would return as happy and relaxed. Not injured, not missing, not dead, not _changed_. She was desperately afraid that John was beginning to suffer from all of those close calls that he managed to survive. Of course, the rules of everything that she knew didn't apply here. The rules of life on Earth did not have much bearing on the life they all lead on Atlantis. John could be telling the truth, she was sure that he at least believed what he told them. _What if he was?_ _What did that mean for them? _

Carson wasn't quite convinced that John wasn't suffering from some kind of delusions, but allowed him to recuperate in his quarters. _Thank God for small favors_, John thought as he walked purposely towards his quarters. He hoped that there was some sort of clue that he wasn't supposed to be here either, that he really wasn't crazy. Why did it keep coming back to that? Sure his brains had been scrambled so many times that Carson had told him that he wasn't even sure how he could even be functioning, but he wasn't crazy, he was sure of that. _What was it they said about crazy people, that they always thought that they were sane? _

John was very careful to not pass through too many public areas, he didn't want to attract too much attention. Like any good story, his had spread through the station like wildfire and he was getting strange looks for the enlisted and scientists alike.

He hoped that he would somehow run into Teyla, to get some reassurance from her that everything would be okay, somehow. Carson had told him that she spent half her time with her people on the mainland as their leader and half serving with his team as ambassador. That was little bit different than what he was used to. His Teyla was on Atlantis full-time, and in more of a soldier and advisor capacity. Teyla was set to return today based on the news of his situation. He wanted to, _needed to_, talk to her. He finally got to his quarters and thought the door open. Thankfully, it obeyed and he slumped onto his bed.

He hadn't been aware that he had fallen asleep until he felt himself being shaken gently awake. "John, are you awake?" He heard Teyla's voice ask. A small smile crept onto his face before he could stop it.

"Hmm? Yeah, yeah, I'm up. Hey, Teyla, what's shakin'?" He struggled to sit up, he felt as if he had sand bags on his shoulders keeping him from getting upright. He opened his eyes and looked at her. She was wearing full-length robes and her hair swirled around her head like a lion's mane. He restrained himself from touching it. She never looked so beautiful. This world certainly agreed with her.

"I came to see how you are, John. May I?" He nodded as she sat down next to him on the edge of the bed. "Tell me of your tale."

He spoke of all of his experiences since he started down this path he could not control, even telling of the child and their relationship. She did not even raise an eyebrow to his admittance, but urged him to continue. He left no detail out. Upon coming to this exact moment in his journey, he felt drained and relieved. He closed his mouth and waited for her response.

"It seems to me that you are being tested by the Ancients, for some higher purpose. Perhaps it is not for us to understand or even to know what it is. Tell me, John, what have you learned?"

_Good question._

Rodney stared at his computer monitor, willing the data to make some sort of sense. He tried to plot all the time frames that John described and tried to discern some sort of order. _Order from entropy?_ He sighed loudly in frustration.

"Careful, Rodney, you don't want to let too much of the hot air out of your head. It might sag." Radek jabbed as he stood behind the frustrated scientist, reviewing the data over his shoulder.

"You know I hate it when you do that. Here look at it for yourself." Rodney shoved the laptop at Dr. Zelenka.

"Why are you looking at EEG readings?"

"What? An EEG?" Rodney turned his head slightly sideways and looked again at the output on his computer screen.

"You know, tracings of brain wave patterns, electroencephalograms, represent the different stages of consciousness of the brain. I do read up on other subjects you know." He responded to Rodney's skeptical expression. "Why are you looking at that? Isn't that more of Carson's arena?"

_Holy shit_. Rodney turned the monitor sideways and it did seem to resemble something of that nature. He grabbed his laptop and took off for the infirmary. Last time he had seen this… He needed more information and Carson was going to provide it if he liked it or not.

John looked around his room as if inspiration was written on the ceiling or something. He shook his head slowly. "I don't know. I don't understand."

Teyla smiled that gentle smile of hers, patted his hand, and stood up. "I have a meeting with Dr. Weir. I will come back before I leave later this afternoon. Do not worry, John, everything will be clear in time."

He watched her leave and he wondered if she was right. He sighed and glanced back up at the ceiling.

"Carson, does this look like a brain-wave tracing to you?" Rodney practically plowed into the doctor, who thankfully, was not in the middle of a treatment.

"Rodney, slow down. Now what are you on about?" Rodney shoved the open laptop into Carson's hands.

"Look, see. What does this look like to you?"

"Aye, I guess it could look like EEG readings. That's got you so worked up? Where did this come from?" Carson looked up from the screen and noted the anxiety that was radiating off of the scientist.

"It's an extrapolation of the data that John was describing from his _travels_. I was trying to determine if there was some sort of relationship between the time periods he experienced and how long he was in each. This graph shows the relationship that the data points seemed to have to each other. Could be a complete coincidence, but you know how I don't believe in those." Rodney got out almost all in one breath.

"Here, let me have a closer look. Okay, if I knew nothing about where the patterns came from, I would assume that the person they came from was unconscious or in a coma. See how the line is pretty flat here; this would be where the alpha and beta waves would be active of someone who was conscious. Here, in this portion, you see an increase in activity, representing the gamma and theta waves, usually seen in people who are in active REM sleep, utilizing some of their memory, but dreaming. So this person's EEG, if you will, shows active subconscious and some memory usage, but not much in the conscious mind is active. Does that help?"

"I'm not sure. I'll get back to you. Thanks." He grabbed his laptop and strode out of the infirmary.

"You're welcome, I think." The Doctor shook his head and continued his chart review.

Rodney's mind was reeling. The last time he saw brain wave patterns was when he was monitoring John in those Ancient virtual reality pods, when they had a run-in with that Wraith. That ship had been destroyed. Everyone in the pods was dead, including that damn Wraith. He mentally reviewed his activities while on that Ancient ship. John had spent a lot of time in those pods. Maybe it had screwed up his head or something, maybe it exposed him to something that allowed his travels. _He_ had spent some time in those pods, why hadn't he experienced any of this stuff? John had been in there longer and John had the Ancient genes, _the real ones_. Would that make any damn bit of difference?

_Maybe it made all the difference. _He slumped onto a bench in the hallway outside of his lab. _All the difference_. He had some data to analyze and a Colonel's brain to pick.

John was trying unsuccessfully to actually complete a meal in the commissary without interruptions. Nobody had actually talked to him, but he felt the stares of everyone who walked by his table. _Okay, let's not get too paranoid now. _

"Colonel!" John dropped the spoon containing his last bit of Jell-o as Rodney screamed at him.

"What? I'm trying to eat here or hadn't you not noticed." John gave Rodney a small smirk as the scientist sat down across from him.

"I think I may know what's going on with you. First, do you remember having spent some time on an Ancient ship in their virtual reality pods?"

"Yes, the ships had been destroyed, everyone's gone."

"Do you remember a Wraith who had inserted himself into the role of the second officer?"

"Yes, where are you going with this?" John's curiosity was certainly piqued at this point.

"Okay, try to follow. When would you say that that was around the time that you began to experience these "jumps"?

"Uh, I hadn't really thought about it much. With all the jumps into different realities, I'm a little fuzzy on when I made the switch to _sci-fi la-la_ land. I don't really know what's real and what's not. So, maybe you can help me on that one." John shifted nervously in his seat. He really didn't know and that scared the hell out of him.

"My guess is that it had something to do with those pods. Here you were interacting with real Ancients and Ancient technology, in some kind of altered state of consciousness. Maybe something was changed or _activated_ by your experience. Maybe a result of or in conjunction with your Ancient DNA. Carson did say that you had an increase in protein levels in your blood that couldn't be traced. I'll leave the medical junk to Carson. The thing is I spent some time in those pods, too. I got the genes, but they're not naturally occurring, as you know. I haven't had any experience like those you've described or met any Ancients that I can recall. What do you think?" Rodney sat back, clearly pleased with himself.

"Just how did the all-seeing, all-knowing Dr. McKay figure this out?" John leaned forward.

"Well, Zelenka took a look at an analysis that I was conducting on all the places, dates and lengths of time that you've described in your travels. He said that he thoughts they looked like EEG's. Just like the EEG's we recorded on you while you were in those pods, to make sure that you were okay. Hmm, maybe we can compare the EEG's that we did record on you to that of the pattern generated by my analysis…." He began typing away on his laptop again and John relished the respite.

"Zelenka, huh? So it wasn't all you then?" John felt the need to needle Rodney, just a little bit.

"He just suggested something that I used to generate my brilliant hypothesis. It was nothing, Okay, here we are." He turned the laptop around so John could view the screen.

"What am I looking at?" John looked with confusion at the jagged lines streaking across the screen.

"The top red line represents your EEG, the one we gathered as you entered the pod, pretty normal. The black line represents your EEG as you were in the virtual environment for some time. See the differences? The red line is up where the black line is down? Those changes represent the parts of your brain that govern consciousness, red line, and subconsciousness, black line. Now to compare to the data extrapolation…" he typed in a few more commands and a third, green line appeared.

"Hmm, interesting. I'm not really sure what this means, but the green line seems to both the red and black lines in a few places. Maybe Carson will have some idea of what this means. C'mon, we're going on a trip to the infirmary."

"You're admitting that you don't know something? That is interesting." John smiled and followed the scientist out of the commissary.


	8. Chapter 8

**Part VIII:**

"Rodney, I would _love_ to help you, but I have work to do just now. Why don't you go bother Dr. Heightmeyer, she would certainly have some ideas on the subject. Now shoo! I've got people to doctor to!" Carson groused when he heard Rodney's request for information. SGA-4 had just come from off-world with some weird rash, they were all scratching their skin practically off. John wanted out of the infirmary as soon as possible anyway.

"Dr. Heightmeyer, I wondered if we could have a word with you." Rodney tried his tact to get in to see the base psychologist.

"It's lucky that I'm in between appointments then, isn't it?" She turned and smiled at John. "Oh, Colonel, I wanted to talk with you anyway. We can set up an appointment before you leave." She didn't really ask him if that was what he wanted. She turned to Rodney, "Now, Dr. McKay, what can I do for you?" He had a sneaky feeling that Elizabeth had not suggested that she meet with him, just strongly encouraged it.

Rodney pasted on his best smile and opened his laptop to show Dr. Heightmeyer his graph. John decided that he would rather poke his own eyes out than study that damn thing again. Let Rodney investigate the crazy patterns, he wanted no part in it. He just wanted everything to go back to normal. He sat down in one of the reception area chairs and sighed.

"John, are you unwell?" Teyla asked.

"No, nothing like that. Just frustrated is all." He looked up into her concerned eyes. "What are you doing here? Is everything alright?"

"I am fine as well. I wanted to speak with Dr. Heightmeyer regarding a conflict with two of my people. I wished to gain her perspective on the situation. Is she otherwise engaged at this time?"

He smiled at her use of such proper speech. He always enjoyed that quirk of hers, it never seemed to change through all the years that he had jumped through. "Uh, McKay's in there with her….it's about me." He added quickly as she raised her eyebrow. Evidently, even here Rodney would not willingly speak with Dr. Heightmeyer about his own problems. He could never admit that he needed help on anything.

"Yes? Has there been a development?" She sat down next to him.

"Well, I guess you could say that. Rodney has some crazy idea that somehow the pattern of my jumps are related to a EEG reading. It's a pattern of electrical readings from a person's brain, showing if they're awake, asleep. Something like that. Rodney had some idea that it was somehow related to the time I spent in the Ancient virtual reality pods." He stopped. "That sounds ridiculous, doesn't it?"

"No, John, I think that only exploring all the possibilities will help you find the answers you seek. I will check back with Dr. Heightmeyer later. Good evening, John." She stood up and strode out, her robes swishing behind her.

John sighed again. He felt as powerless and clueless as he had every time before. At least he had been able to stay here for a little while. At least Rodney felt that he was making some progress in figuring this mess out.

"Colonel Sheppard?" He heard Elizabeth call over the comm. headset.

"Yes, Dr. Weir?"

"Can you come to my office?"

"On my way." He practically bounced out of the office, he was glad to get the hell out of that office and work on something more station-related. Well, at least he hoped that it was.

"Dr. McKay, as Dr. Beckett told you, I have some expertise in this area. I did go to medical school, too." She laughed, a sound that Rodney was absolutely sure that he had never heard before.

"John, how are you feeling?" Elizabeth asked as he entered her office.

"Good, I'm good. What's up?" He swung himself into a chair facing her desk.

"Information Systems Security has requested your _special_ assistance in upgrading security measures in the main computer system. It seems that they have come across a few Ancient safeguards that they are not able to get through."

"Don't you think that Rodney may be better equipped to handle that? I'm not really all that technically-oriented." John leaned forward, studying Elizabeth's eyes. Something flashed through them as he pushed back on her request and then it was gone.

"I will ask him to join you, but IS Security needs some of your command codes to get into the locked areas in the system. I just don't have the time right now to help them, plus your Ancient genes may help. Would you mind heading over for a few hours? I don't want to over-tire you, Dr. Beckett would have my head." She laughed lightly.

"Uh, no, I think that I will be okay. I can just grab Rodney on my way if you like." He started to get up.

"That's okay, John. Like I said, I'll send him along after he gets finished with Dr. Heightmeyer. Thanks." She looked back down at her laptop as she finished her sentence.

He had the distinct impression that he was being dismissed. Elizabeth must have taken a page from Caldwell's book when he was here. He certainly didn't _dismiss _people when he was done talking. He kept thinking about it as he made his way to the South tower. Someone must have told her that Rodney was gibbering about that stupid EEG pattern with the psychologist, he was pretty sure that he hadn't mentioned it. Maybe Carson, since he was the one who suggested that they stop in to see her. He'd have to catch up with Rodney soon anyway to see if he had made any progress. Rodney was the only one who didn't think he was crazy. John should stick to Rodney like glue. Well, he'd had enough of that scientist for awhile. Let the psychologist drain all of his mental energy.

He was starting to feel fatigue setting in as he came to the IS Security detail set up at an information node in the South tower lobby. "Lieutenant, Captain." He acknowledged their ranks, but couldn't for the life of him remember ever having seen them before.

"Colonel." They answered in unison.

"What do you need me for?" He asked, stepping up to the console.

The captain began explaining the purpose of the security upgrade and why they were having so much trouble getting past some Ancient equivalents of firewalls. John nodded where he thought was appropriate places, but really didn't follow anything of what was being said.

"What do you need me for?" He asked again, hoping they would abandon their explanations and get to what he was supposed to do. He was rapidly losing energy and patience.

"We need you to enter your command codes to open this security grid. From there we can add some upgrades and hopefully will prevent any data from being lost if we were ever subjected to another Wraith attack, sir." The lieutenant added.

"Okay." A feeling in the pit of his stomach was begin to brew. Suddenly he wasn't liking this plan. "And Dr. Weir is aware of what you're asking me to do?"

"She requested that you participate as she was unable to. Are you feeling okay, sir?" Now the Captain was trying to convince him to participate.

"Yes, Captain. I'm good. " He began scanning the laptop's output report and his eyes stopped on the blinking cursor. He typed in the first-level access codes to get into the secure server. He would type that normally three or four times a day to get into the Atlantis system. It was accepted, although it took a little longer than he normally expected. He typed in the second-level username and password that allowed him access to all higher-level security functions, including personnel, medical, and inventory. He probably only used that once or twice a day to check the status on the running of Atlantis. Normally, Elizabeth and Grodin would handle this stuff. He only filled in as back-up when needed. Again, he noticed a slight delay when he entered the data. He looked up at the Captain and the Lieutenant expectantly when nothing happened on the screen after he entered his last data.

"This should take a few minutes, sir. The system's uploading some of the new components now." He had stopped paying attention after a minute or so. The two of them were so focused on the screen he figured they wouldn't mind if he just leaned up against the wall for a few moments. Exhaustion was really sapping his strength. He then noticed that Rodney had never made it down. He tapped his comm., but nothing happened. _Damn, was the battery dead or something?_

"Uh, could either one of you lend me your comm.? Mine seems to have quit." He walked towards the pair of officers and looked over their shoulders at the screen. He stopped talking when he recognized Wraith characters scrolling down the screen.

"Dr. McKay, I see where you may have seen patterns generated in this data, but that they representative of actual EEG's is absurd. Here, let me show you an actual EEG reading. _Yours_, actually. All Atlantis personnel have those included for comparison in case anything unforeseen should occur. See? You can see that the actual EEG shows much more detail. Do you remember when this was taken? They asked you about all sorts of long-term and short-term memories so record the different spikes. Here is when you were asked to sleep over in the sleep lab. You can see where the differences between the conscious and unconscious brain activity. Is there anything else? I have patients." She seemed to not be in such a good mood anymore.

"Thanks for your help, Doctor." He _did_ see similarities and he wasn't so ready to give up on the connection. While he was on his way out of her office and she was reviewing her next appointment's files, he grabbed his file and slid in into his closed laptop and left.

Rodney walked deliberately to his lab when he realized that John had not been in the waiting area where he had left him…he glanced at his watch…_an hour and a half ago_? He tapped his comm. to find where the errant colonel may have gone off to when he ran into Elizabeth in the hallway. "Elizabeth?"

"Yes, Rodney? I'm sorry, but I can't talk right now. I'm late for a meeting. What can I do for you?" She did seem quite harried.

"Um, have you seen the Colonel? I have some information he may find interesting." For some reason, he felt himself holding back information about his suspicions. He needed to review them with Colonel Sheppard first.

"No, I haven't seen him all day. Perhaps he's checking in with Carson in the infirmary. You may try there. I've got to go." She rushed off without an offer to help him.

He was little peeved with Elizabeth's cold treatment. She wasn't normally so abrupt with him. He tapped his comm. again to try and raise Carson or John, but it didn't seem to be working. _Strange._ He looked up and down the corridors looking for someone to ask about the comm. system, and thought that he should just pop down to the infirmary and check with the doctor. He would surely know where his star patient was.

John began to feel a little dizzy and the edges of his vision began to go fuzzy. His heart rate shot up as he glanced around and thought he saw a Wraith, or a shadow of one anyway. He shook his head in an effort to clear his vision. He looked again at the two military personnel and at the screen they were so intently staring and saw regular Atlantis logos and a mixture of English and Ancient characters, just like was supposed to be there. He blew out a breath and weaved about a little more.

"Whoa there, Colonel. Why don't we get you back to the infirmary? Dr. Beckett will want to check you out, sir." The Captain and the Lieutenant took each of his arms over their respective shoulders and helped him back to the transporters. He was so tired that he was actually looking forward to it.


	9. Chapter 9

**Part IX:**

**Sorry, a little on the short side this time. Almost there, folks! Thanks for all the great reviews, you've inspired me to update faster! Love to all of you!**

John didn'tremember actually walking, no- being dragged, to the infirmary. He slowly opened his eyes as he started to roll over in the bed. A painful pinching grabbed his attention and ripped him wholly back into consciousness. _An IV?_ He wasn't that bad. That vicious doctor always liked to stab him with sharp objects whenever possible.

"It's about time that you came around. I'm getting really bored sitting here and staring at you. Where were you? I tried to reach you and nobody seemed to know where you were…" John tried to fall back to sleep to escape the ramblings of one Dr. Rodney McKay. Not so lucky.

"What? What are you talking about? Plenty of people knew where I was. Where were you? I couldn't call you on the comm.'s." John opened his eyes up and looked at Rodney's face, as best as he could when there were two or three of him at a time.

"When I got done with Dr. Heightmeyer, you were missing and I asked Elizabeth and Carson. They didn't know where you were until two military types dragged you in here practically comatose. Why didn't you tell me you were going off somewhere? I was making progress I'll have you know." That wasn't _technically_ true but it made for a more dramatic diatribe.

"Take a breath, Rodney." John lowered his voice. _Something was a little fishy now_. "Now get me out of here and we'll figure this thing out, okay?" John looked around, satisfied that no medical personnel were in the immediate vicinity; he pulled out his IV and pulled off the monitors that were placed on his chest. He reached over and turned the monitors off to make sure no alarms were triggered. "C'mon. I have a feeling all is not what it seems."

Rodney tsk'ed at John's hasty exit, but followed him out to one of the balconies on the central tower. "Now why are we being all CIA counterintelligence?"

"Rodney, _Elizabeth_ is the one who called me out of Dr. Heightmeyer's office."

"What? How can that be? She told me that she had no idea where you were. What was your assignment?"

"Security codes, something about access to some protected areas of the Ancient computer interface. I think that I just gave intelligence to the enemy."

"What? What are talking about? How's that possible?"

"We need to get somewhere safe and defendable. We may have a foothold situation here. I think that I've been compromised. Rodney, you need to make sure that I don't do anything else that could jeopardize Atlantis. Do you understand? I'm not in full control of this situation, or myself. I'm not sure if I could be _jumping_ somewhere else at any time. Or maybe they're all delusions, I don't know. I need to be able to count on you. Can you do that?" John felt as if all the events of the last few days, weeks or whatever it was, were catching up with him, settling in the pit of his stomach. He felt shaky and weak. He hated feeling like that.

"Yes, I have to. I think that Atlantis is at stake. What do you think is going on?"

"I'm not really sure." He slumped down against the wall until he was sitting on floor, facing the ocean. He closed his eyes and listened for a moment. The ocean sounded dead, flat. Maybe his brain was in the process of kicking off and this was the first stage. He chuckled at that morbid thought.

"Colonel, are you still with me?" Rodney's anxious request shook him back into the present.

"Yeah, yeah. Just tired. What do we know?"

Rodney sat down next to him. "Well, let's see, you've been experiencing _jumps_ between what you think is different times and alternate realities and now you think that there's a foothold situation. Maybe we should get you back to the infirmary, maybe Beckett can help you."

"Rodney, I know you don't want this to be true and you're working especially hard to explain it away, but I could've sworn that I saw Wraith data being uploaded while I was helping on getting into the supposed Ancient database. Explain that." John sighed. He hoped, too, that all of this was just a giant misunderstanding, a giant bad dream that he would wake up from any time now.

"You could've been delusional then, too. Did those officers see it, too?"

"Rodney, this may be a stupid question, but have you ever seen those officers before? It could be that they never came in my reality or my brain is turning to mush and I can't remember them."

"Well, you know that I think all you military types look the same to me. That being said, no, I don't really remember them specifically. They must've come in on the last transport from Earth or something. What does that mean anyway?" Rodney huffed.

"They were studying the Wraith data as if they understood it and did not seem surprised in the least to see it on their computer screen. They only stopped when I came over."

"So you're thinking that they're plants or spies or something? C'mon why would a human ever help the damned Wraith?"

"Who said that they were human?"

"_C'mon! Not human_? Don't you think it would be a _little_ bit hard to disguise that skin, those fingernails, the tendency to suck the life out of humans?" Rodney stood up and spun around to look down at John.

"Okay, well, I haven't quite figured that part out yet. What else do we know?" John figured a change in the subject would get the hotheaded scientist to cool down a little bit. He'd had _way_ too much experience calming him down in tough situations.

"Yes, well. That EEG pattern that I developed. Both Drs. Beckett and Heightmeyer did their best to dissuade me from following up on it. And you know what that does to me."

"Makes you want to follow it all the way to the end, doesn't it? That's what I like about you, Rodney. Tenacity. Anyway, go on." John responded, hoping the ego massage would kick-start Rodney's brain into analytical mode a little more. John searched the horizon again. It was starting to get dark and the streaks of the sunset were beginning to caress the surface of the water. He smiled. _God, he loved this place_. Now he had to do everything in his power to save it.

"Well, when you went missing when I was with Dr. Heightmeyer, no one seemed to know where you were. Even Elizabeth. It could've been she just forgot or something."

"Have you ever known her to forget something like that? What else? What about the EEG thingy you mentioned? Do you think that it means anything?" John asked, willing himself to have the energy to keep thinking about this problem and not losing focus.

"I'm not really sure. I'll have to think about it for a while. Do you think that we're in immediate danger? Who do you think's involved? Is it like invasion of the body snatchers or something? That people have been replaced by Wraith look-alikes? If that's the case, obviously they know we're still here. Why haven't they sent hive ships to blow us away? Why haven't they just dialed up Earth and be done with it?"

"Good questions, I wish I knew… Let's get inside. I'm going to collapse soon if I don't get some sleep. You could use some yourself." John grabbed Rodney's proffered arm to pull himself to his feet.

"What's wrong with you exactly? Why are you so weak and sick? Did Beckett ever give you a diagnosis? Oh God, who else is involved in this? Are we the only ones left?"

"Okay, McKay, no hyperventilating on my watch. Again, good questions. I don't have any answers, but I damn well will get them."


	10. Chapter 10

**Part X: Another shorter section. Lots of twists and turns, so keep your seatbelt fastened and your tray tables in the upright position!**

John dropped Rodney off at his quarters after repeatedly assuring him of his safety and making sure that he went to sleep. John felt like he could sleep for years, but he had to get some answers. That meant recon- recon of his people. He shook his head at that thought. He never saw this coming, he always thought that through everything, he could at least count on his team to support him and help keep Atlantis from falling. _He was wrong_. He hoped desperately that he was the one who was wrong about all of this.

Rodney squeezed his eyes shut in desperation of his own. He _wanted to sleep, needed to sleep_, but he couldn't turn his mind off. Why was John still so weak? Carson had said that he couldn't find anything wrong with him. He didn't know if John was aware of it, but John was looking worse by the minute, like the life was slowly being drained out of him. Sure, he would put up a brave front about it and assure Rodney that he was fine. John would say he was fine if his own arm was hanging off and he had a broken leg. Needless to say, Rodney didn't believe anything the Colonel said about his health without a grain of salt or adamant support from the Doctor.

_Why did Elizabeth and Carson both deny that they knew where the Colonel was when John said that they had to have known? Forgetfulness? Covering something up? Goddamnit, they knew that he could never let a mystery stay that way._ He had to chase down every lead to their natural conclusions and solve the problem. Hell, that was what he did and with _flair_, if he did say so himself.

_Why was John _jumping_ all over the place, seeing the future, different versions of the past and present? Was it due to the involvement of an Ancient as John thought? What would be the point? Why has he stopped? _

_How were the Wraith involved?_ John had been pretty sure that he saw Wraith text on an Atlantis laptop, with two officers observing with no obvious problems with it. John swore that he couldn't remember ever having seen those two before, but that could make sense if this John was from another dimension or timeline or something. Of course, he didn't remember them either, but all of the military types looked the same to Rodney. He had checked their personnel files when he had returned to his quarters and they seemed standard issue, nothing out of the ordinary.

_What was he missing?_ _Something that would tie all of this together._

John wandered around as unobtrusively as he could, especially trying to avoid members of the upper level leadership and the medical staff, all of which whom would thwart his plans to prowl around Atlantis, looking for something out of the ordinary. He needed to investigate those two officers, Captain Brown and Lieutenant Smith. _C'mon, Smith and Brown_? Those were the most generic names he could think of. He made his way to a lesser-frequented area of the South tower data station and accessed their personnel files. He reviewed them quickly, scanning for anything anomalous, something to jump out at him. He huffed in frustration, there was nothing weird about either one; their service records read like textbook examples. _What did that mean?_ One, they were regular military officers who were assigned Atlantis and they accepted, based on their average computer programming skills? Or two, _the more paranoid possibility_, that they were plants, spies for organizations unknown. He couldn't rule out either possibility. His exhaustion was suddenly catching up to him and he felt drained. He slowly made his way back to his quarters and slipped in. He crawled into bed and didn't remember falling asleep.

John's dreams were anything but tame normally, but his on this night were positively terrifying. He kept dreaming about being captured by the Wraith and having the life being drained out of him, one excruciating minute after another. In others, it was his team members, Teyla and Rodney specifically, as Ford looked on and laughed. He felt powerless and without options in all of them and he finally woke drenched in sweat as the sun just rose above Atlantis' horizon.

He sat up and mentally reviewed each dream as if they were missions gone horribly wrong and thought about what he should have done differently. No answers came of it and as he stood up to stretch, his door chime rang out. He _thought_ the door open and Rodney stepped through. "So, Colonel, anything new?" Rodney asked lightly, but John could tell that he was holding something back.

"No, not that I can think of. Why, is there something?" John sat on his bed and pulled on his boots and proceeded to tie them as Rodney remained silent. "Well?"

"I'll wait until you're done, this is important."

"Oookay, spill it."

"I don't think that anyone here is a spy for the Wraith or replacements or clones or anything like that. I think that it's _us_."

"Rodney, what the hell are you talking about?"

"I thought about this all night. I know, I know, sleep is good and all that. But I couldn't get all of these questions out of head, you know? You know how I can't turn down a problem or challenge. So, I looked at it like one of the problems that we would encounter here. First, define the problem. Second, figure out what you know. And third, figure out what you don't know. Go from there."

"Again, okay, but you're losing me." John really was losing him, but he knew from experience by feeding Rodney's ego a little bit, he tended to get to his point a little faster and in a more clear fashion.

"I know, try to follow." John nodded in response. "Yes, well, maybe the reason everything is all wonky for you and the reason why everyone seems to be trying to either work against us or worse…_guiding_ us to divulge certain sensitive information. Maybe the reason is, we're the plants in this scenario and we're being pumped for information. That sounds crazy, I know. But think about it, what would be the point of an Ancient helping you, showing you the past, future, and other alternate realities? How much information have you shared with everyone as you've been trying to figure out what's been happening to you? What would that information mean to enemies of Atlantis? Heaven knows how many passwords, security protocols, and other sensitive information you or I inadvertently shared."

"Wait, wait." John put his hands up in surrender. "How do I know what you say is true? How do I know you're not one of them trying to get on my good side?"

"C'mon, Sheppard. Do you think that I would waste my time trying to explain this to you if I were just trying to get you to trust me? Have you noticed anything else weird?" Rodney stopped to catch his breath.

"Weird? Everything here is _always weird_. Don't you think that we should be looking for things that were too ordinary? When do we ever get _ordinary_?"

"Like what?"

"Like Smith and Jones for one. Their service records were too regular, too ordinary. Never grab anyone's attention. How would they have been tapped to go to Atlantis? Didn't you notice that?" John tried not to look smug when he saw the scientist's face fall a little.

"Well, um, no. But, I wasn't looking for it of course, and I'm not military. I'll leave that stuff to you." Rodney recovered his pride a small amount.

"How do explain the fact that _I've_ been jumping all over the place and _you_ haven't noticed anything different?" John was beginning to buy into this theory of Rodney's.

"Like you said, you're more suspicious of something that's too regular or ordinary, so they gave you an adventure, a huge mission, if you will, to carry out. Then they just sat back and waited for you to complete your mission, follow your training. For me, they left just enough breadcrumbs for me to follow and be distracted from what was really going on. The whole EEG suggestion from Zelenka when I was starting to ask too many questions about your situation. Getting me to talk to Heightmeyer so you could get pulled somewhere else without my noticing. _Very, very slick_. They just didn't figure on _my_ figuring it out."

John looked around his quarters, thinking about where the cameras or the bugs could be hidden. It may not matter where they've been; they had been watched the whole time. Rodney noticed that the Colonel began searching his room and he placed a hand of John's shoulder. "It doesn't matter, we're not really here."

"What? Of course we are. I can touch you and everything else around here. I can think and I feel the same. What do you mean 'we're not really here'?" Realization dawned over the Colonel's face. "_We're still in those damned Ancient artificial reality pods, aren't we? Everyone here is a Wraith, huh_?" John sat down hard on his bed, cradling his chin in his hands.

"_Bravo_, Colonel, I didn't think that you'd come to that conclusion just yet. And yes, I don't think that we've ever left those pods. That everyone here is a Wraith or at least programmed to collect sensitive information. They may not even know that they aren't real. The Wraith could have found that ship, programmed all the intel they had and left it for us to find. We played right into their hands. What blows me away is how detailed everything is, everything just perfect. Did they perfect mind-scanning techniques or something?" Rodney started to look around the Colonel's room with a new appreciation for virtual reality constructs.

"They didn't have to, somehow they've tapped into my Ancient gene capabilities and have been able to influence me to a very great extent. They could have just convinced us that everything we see is just how it's supposed to be. You have the Ancient gene, too. But since it's not natural, maybe they couldn't affect you in the same way. Somehow, one of the Ancients must be involved here, maybe that's how they are making these connections."

"Hmm, makes sense. Big problem, though. We don't know how long we've actually been in here and if those involved can communicate with the outside world. If so, Atlantis is in great danger." Rodney started pacing.

"They'll know that Atlantis wasn't destroyed and they'll come back to finish the job and get to Earth."

"Precisely."

"We need to get out of here."

"And that worked so well last time."


	11. Chapter 11

**Part XI: Thanks to all of you for your patience, I had a little bit of writer's block. There will only be one more part after this, the finale! Thanks again and please review! **_(A wee bit of rough language so be prepared)._

John stared out of the window of his "room" at the ocean.

Rodney came up behind him, "So what's the plan? How do we get out of here, _alive_?"

"You're the resident genius. Haven't you thought of anything yet, _Einstein_?" John snarked back. The words didn't quite cover the anxiety he was feeling over their realization. He didn't feel any better in his situation now than he had when all of this started happening. Loss of control and one pissed off Lt. Colonel do _not_ mix. He scowled at that thought. Rodney shot him a look that gave John pause. "Sorry, a little frustrated by all of this. A prison with no walls, but still no way out that we can see."

Rodney nodded and stared out past him, observing the ocean. "There's a way out of every prison."

"You hope." John sighed. He was rapidly losing what little patience he had left.

"C'mon, don't you think that whoever or whatever designed this system had to include some sort of safeguards, _back doors,_ if you will, in case the situation in here got a little hinky?"

"Where would our friends put the _back door_?" John grabbed his P-90 and all the ammunition he could find into shoved them into his pockets. "And who says they're the only ones who can control this damned virtual environment?" He slipped out into the hallway, which was now darkened, lit only by emergency lights.

John's head was beginning to buzz again and he started to feel very uneasy. He looked over at Rodney who seemed to notice that the environment around them was beginning to change, almost feeling colder somehow. Not in temperature, just a feeling. "You feel that?"

"If by _that_ you mean that you think that they're on to us, I think you're right. Sheppard, I think we'd better move!" Rodney took off down the corridor faster than John had ever thought was possible for the scientist, but hell, this wasn't the real world anyway. _Wasn't anything possible? Wait a goddamned minute!_

"McKay, stop where the hell you are! This is stupid, we can't get anywhere by running. We are in one giant Atlantis-shaped box, conveniently sized to fit in our heads." John walked as quickly as he could, without jarring his head too much, to catch up to Rodney. "We're not safe or protected anywhere. We need to take control of this, right here and now." He leaned against the wall of the hallway and dropped his P-90. "Our brains were not made to stay in here this long, especially when it was designed for Ancients. We don't really know if the Wraith are involved or not, we only got that from when we thought we had discovered what has happened on the Aurora the first time. We need to speak to Elizabeth and Carson, for starters. They seemed pretty decent about dealing with us before, maybe we could convince them that we need to leave. They must know by now that we've figured this out. Maybe we can negotiate."

"Are you mad? _Negotiate, my ass_. They have us by the _balls_ in here. We have nothing to bargain with without giving up the most precious thing we have. What motivation would they have to let us go? Why do they have us here in the first place anyway? _For information on Atlantis_, that's why. Do you think that we could just walk up and ask to be let go and they'll say, 'okay'?" Rodney's started to rise in both volume and pitch as he wound up his tirade, his arms flailing in time to his crescendos.

"Calm down, Rodney, getting upset is not going to solve anything. Okay, no negotiations. I was never very good at those anyway. Fighting, yes, talking, not so much. Especially not you. I think you've managed to insult every new civilization we've come across. If these beings are Ancients or Wraith or something in between, we need to stay civil. Understand?"

Rodney looked at him, his mouth opening and closing like a fish, with no sound.

"I'll take that as a yes. C'mon. I need somewhere quiet to think for awhile." John dragged a still spluttering McKay down the hall to one of the piers that was not being used in there Atlantis. Hopefully, it would be the same here.

"Maybe we need to think outside the box. How would we find one of these back doors? Can we cause it to find us, maybe?" John leaned over the railing, closing his eyes as he felt the wind ruffle his hair slightly. He breathed in deeply. "Pretty hard to believe that this isn't real, huh?" Rodney nodded but remained uncharacteristically quiet. "You okay, Rodney?"

"If by okay you mean _screwe_d, then, yes, I'm okay."

"Rodney, we will get out of this, you know." John placed his hand on the scientist's shoulder, his attempt at comfort.

"I'm glad that one of us is optimistic. I think that we are Wraith food being kept warm until needed." Rodney stated quietly.

"It's probably more like blind stupidity, but yeah, I think that one way or another, we'll get out of this."

They must have been out on the balcony for several hours as the sun was beginning to set, setting orange and pink streaks across the water. He was brought back to the present by the rumblings of his stomach. "McKay, do you think we need to eat in here? It probably doesn't really do anything for our _real_ bodies, huh?"

"Oh great, just great. I didn't even think about that we are probably starving to death in those stinking pods. What are we supposed to do?"

_Shit, I probably should've kept that thought to myself_. John sighed and scanned the waves again. _Hmm, starving to death. Could we potentially make that a little more figurative and faster? _"Okay, Rodney, you're not going to like this, but I have an idea."

"Famous last words." Rodney ripped open a Powerbar and chomped into it, even though he knew it was only in his head.

"Well, you're definitely not going to like this, especially if it doesn't work. Because then, you'll be here all alone and have to deal with this crap yourself."

"Alright already, what's the brilliant plan?" Rodney wasn't paying attention as John swung his leg over the railing and the other until he was standing on the other side, facing the raging ocean. John glanced down and realized that they were higher up than he had originally thought.

"Well, since I've gotten pretty close to this without actually not having done it, I'm going to kill myself and get out of this godforsaken game. If nothing changes, don't do this yourself. If everything changes, it means I got out and changed it. You'll have to jump yourself, unless you want to go another way. Death by lemonade, if you prefer."

"WHAT? Oh no, you're not. You've cracked! This is all a big game to you, isn't it? You can't do that!" Rodney scrambled towards the Lt. Colonel as he leaned forward and fell forever.

3


	12. Chapter 12

**Part XII:**

His next awareness was shot through with a bright, white light encompassing his whole vision. He thought recklessly for a minute that he was dead. Then as suddenly as it appeared, the light was gone and was replaced with the faces of a few familiar people.

"Hey, there, how are you feeling? We thought we lost you there." The Doctor's warm hand ran over his forehead. He smiled when he heard Dr. Beckett's voice cut through the buzzing in his head. "You're probably feeling a wee bit poorly right now. You were dehydrated and your electrolytes were all over the place…"

"He's awake?" Elizabeth stepped into his view and he let out a breath he didn't realize he had been holding. For some reason he knew that he was on Atlantis, the real one this time.

"Wh..?" He tried to find his voice as someone slid a straw into his mouth and he drank for a good thirty seconds. _What the hell happened?_ His grip on consciousness seemed to be very tenuous and he slid back into the darkness again for a time.

He became aware again of some disembodied voices, some feelings of being touched on his arms and face, and vertigo. He felt as if he were on the deck of a ship being tossed around in a particularly bad storm. He groaned and prayed that he wouldn't throw up.

Again, the lights ripped him out of a very comfortable dream of Earth and he growled in protest. "Lemme sleep…"

"Open your eyes for me, please. It's Dr. Beckett. Do you know where you are?"

"The same damned place that I've been for weeks. Atlantis, of course." He scraped his eyes open again and the worried face of the doctor swam into his view. "What happened? Why do I feel like death warmed over?"

"You were in one of those damned Ancient AR pods, remember? When we couldn't get the both of you out without running the risk of brain damage, we removed the pods and brought them here to Atlantis for study. For a safe way to get the two of you out. That was two weeks ago. We've done our best to keep both of you alive and Zelenka and his team were working around the clock for a way to free you intact. Do you remember what happened?" Elizabeth asked as gently as she could. "Rodney, do you know what happened to John?"

Rodney's eyes flew open. "What do you mean? He..he's not awake yet? Why am I awake? I didn't do anything." He felt color rushing to his cheeks as the panic rose in his chest. He sat up and looked around the infirmary. "Where is he?" He turned to his left and noticed the Colonel, very pale, unmoving, and attached to more tubes and machines than Rodney had ever seen. "Why is he like that? What's wrong with him?" He attempted to get out of bed, but his legs felt like rubber.

"Rodney, wait. Please lie back down. I'll answer your question but you need to settle down." He felt himself being placed gently back under the covers and heart monitor leads being replaced. "Just to make sure that everything's okay. Don't worry, I won't let anything happen to you."

"About fifteen minutes ago, both your and John's monitor alarms went off indicating an elevated heart rate. By the time I came over to investigate, you were coming around. Sheppard, on the other hand, has slipped deeper into a coma." Dr. Beckett explained to the visibly shaken physicist.

"John killed himself in there to save me, that's what happened. So, I woke up and he probably won't ever wake up again." He sighed a deep sigh and turned his head to watch the ventilator push John's chest up and down at regular intervals.

"There'll be time for explanations later, Rodney. You get some rest. We'll talk more in a little while. John's still with us and I intend to keep him that way." Carson checked Rodney's stats one more time as the scientist's eyes slipped closed once again.

John heard every word that Rodney and the others had exchanged, he was able to fight his way back to almost consciousness, but not quite. Not enough to open his eyes, not enough to move even his little finger. He was a prisoner in his own body. He could hear the rushing air from the ventilator as if was pushed and pulled from his unwilling lungs. It seemed to reverberate in his head and fill his ears, like ocean waves crashing. He wondered if this was what it felt like to be Atlantis, surrounded by the sea, protected and trapped at the same time. He let his mind wander because if he thought too much about his situation, he was afraid that he would go crazy. He decided that he would either get all the way better or he would will himself to slip away, he couldn't stay like this. He seemed to be aware that time would flow slower and faster, perhaps he was only aware of his surroundings for short periods of time. The next he knew, it seemed to be nighttime. He knew the schedule of the infirmary almost as well as he knew the habits of his teammates. It was very quiet; he could hear the thumping of his own heart and the whooshing of the ventilator. He thought that he could hear the quiet footsteps of the nurse on duty every now and then, coming over to check on him.

_Move, dammit, do something so they know you're in here! _ He willed his arm, his fingers, something to move when she was near to let the nurse know, to let anyone know. He wanted to scream in frustration, but all he could do was scream in his mind. He counted from ten, forcing his mind and body to calm down, there's no point in a fight-or-flight reaction when he couldn't move. He was glad on some level that his sacrifice, if that was what it was, in the AI environment could get Rodney out. He wasn't quite sure how his "killing" himself in there would push Rodney out, but he was ecstatic it did. He didn't need anyone else dying because of _his_ actions. Plus, Rodney was the one who could figure out all of this anyway. Too bad his potential savior was incapacitated in the bed next to him. He would just have to wait, he didn't have any choice.

He started to let his mind wander again when it started. It was just a funny prickly feeling along his spine and the back of his head, but it quickly bloomed into excruciating pain. He couldn't move, couldn't do anything. His body suddenly arched up and started shaking uncontrollably. Everything went unbearably white behind his eyelids and then nothing.

"He's seizing!" Rodney was ripped out of a deep sleep to see the collection of medical personnel surrounding the Colonel's bed. Rodney held his breath and listened.

"His heartrate is up to 170 bpm! Respiration 100. BP: 180/100. He's going to stroke out if we don't get this under control," Carson's voice raised above the din. Rodney strained to see what was going on. Sheppard's face was bright red, shining from sweat. Several personnel were attempting to keep him down on the bed. Carson was injecting something into the IV port on Sheppard's arm. "That should help. Okay, okay, there we are. He's stabilizing. Monitor his vitals, we'll need a CT scan as soon as possible."

"Carson?" Rodney managed weakly.

"Yes, Rodney?" The Scot was already standing next to his bed.

"Is he…?"

"We've stabilized him for now. He seized, most likely a result of the removal of the AI integration input in his brain. He should be okay for now, we're monitoring him closely." He looked at Rodney's pale face. "No, Rodney, you're not in any danger of that. You seem to be recovering quite well. Get some rest, the Colonel is holding his own."

John had never felt so worn out in his whole life. He prayed for unconsciousness. He didn't want to be aware of that ever again.

Rodney was next aware of sunlight streaming in through one of the side windows, making the inside of his eyelids an unpleasant orangey-red. He sighed and pried his lids open. The infirmary was quiet, probably still early. He turned his head slowly to see if he could tell how John was doing. The ventilator was still making that awful hissing noise and the soldier's chest rose and fell in time with it. John looked so empty, like the part of him that made him _Sheppard_, was gone or at least in a very deep sleep. All he could see was a shell. _  
_

He pushed himself into a sitting to better see what was going on. He realized that he hadn't thought about his work, his laptop, his lab for a long time now and that was okay. Everyone was replaceable, at least at some level. He blinked back some moisture that had somehow made it into his eyes. Since when did he allow himself to be so maudlin? He laughed to himself. He knew that he was the only one that could break Sheppard back into reality. He needed to get to work. He slid out of bed and made his way out of the infirmary, aware that the watchdogs would be on him soon enough.

John swam back to the highest consciousness that he could manage and unfortunately, that still meant no movement, no communication. He could hear, though, and feel, and he guessed that was something at least. He forced himself not to panic when he realized that this could be permanent, a living death. He hoped that someone would have to grace to put him out of his misery sometime. Not just yet. He still had a little hope that he could get out this. He heard snatches of conversation sometimes using words like "irreversible brain damage,…never wake up,…persistent vegetative state" and he prayed even harder for s solution.

Elizabeth stood on the observation deck overlooking the inactive Stargate, chewing her lip unconsciously. _It was funny_, she mused_, the problems we had envisioned before we left our system, turned out not to be the problems we have had to deal with in frightening regularity_. Her second-in command of sorts, her friend, lay in a coma, perhaps never to come out and her top scientist lay recovering from an event that she never had thought about outside of those sci-fi dramas her college roommates used to watch on TV. _If they could only see her now_. She strongly resisted the urge to call Carson again and ask for an update. She had bothered him enough; he looked about ready to pass out himself. She'd give herself an hour before making her way back down to check in on everything. She scanned her computer screen and noted that only two teams remained off-world. One of which had Teyla and Ronon. both of whom would be pleased that Rodney was awake. She tried not to check her watch and just resigned herself to watch the ocean.

John was startled back to consciousness when the deep rumbling of Ronon's voice filled his ears. He felt the soft hand of Teyla in his own. Ronan was telling him about their latest trip and some of their exploits. Teyla was lightly stroking the back of his hand. If he could purr, he would have. It was the best he had felt in a long time, even if he couldn't move. He tried not to think past the moment and mentally shivered in the pleasure of her touch. It felt really good to have his team back together and he really felt part of it. In what seemed like moments later, he heard Elizabeth and Rodney talking about his experiences in the AR chamber. At least he could have some entertainment for a while, he was getting bored and frustrated with all of this inactivity.

Hours, days, weeks, passed along from what John could ascertain. He seemed to only be present for short periods of time each day. He spent the few moments of clarity trying to make himself move or speak or something to let them know that he was there. _Not to give up on him_. He had been moved to another quieter part of the infirmary, he guessed to allow for more space for active patients. He had heard snatches of comments about his going back on the Daedalus and back to Earth for long-term care. He screamed in his head to Elizabeth, to Teyla, to Rodney, or anyone on Atlantis not to let that happen. He knew that if he left, he was never coming back, in all sense of the word. Doctor Beckett always lent his gentle touch to the Colonel's care, always trying to keep him in the loop of what was going on in Atlantis. Teyla sat with him and read or told stories or even once in awhile graced him with a song from her homeworld. Ronon would stop by, Cadman, and many others, but as time passed, the visits became fewer and further between. Elizabeth made a point to stop by every other day to see him and update him on her activities, off-world negotiations, anything she thought he may be interested in. He appreciated those visits like a dying man appreciated water in the desert. Those visits kept him sane. It would have been so easy to just let go and separate himself from this world. He wondered sometimes if that was what it was like to ascend. He didn't want to ascend, _dammit_, so he kept surviving until he wouldn't be able to anymore. Rodney didn't come by very much, Elizabeth had let it slip that she thought he felt guilty for coming out of the AR while he didn't. He knew that Rodney would continue to work on this problem until he solved it. He could always count on him like that. He would make it up to the scientist if it were the last thing he ever did.

Rodney ran simulation after simulation from the AR pod that he had spent several weeks in, hoping for a reason why he came out of it and John didn't. Most of the scientists had just learned to stay out of his way. He did go by to visit John; he just stayed out of the way, somehow afraid that John would sense his guilt. The truth was he couldn't stand to see John like that, just a shell. He felt as though John was already gone and they were just waiting for his body to die. Even if that was all he could help with, he was determined to bring John out of the artificial reality even if it was only to die. Nobody deserved to be trapped in one's own body. He knew in his heart it was what John would want. Of course, that would be the last resort. His real goal was to bring John out alive and able to function normally. He gulped down the rest of the rapidly cooling coffee that some lab assistant had brought him earlier and rechecked his calculations.

John opened his eyes slowly and blinked hard against the blinding white light that surrounded his bed. He realized that he was still in the infirmary, but felt pretty good. He sat up slowly and scanned the room. Empty. All of the equipment that he had heard was keeping him alive before was gone. He shook his head to clear his vision and swung his legs over the edge of the bed. The floor felt a little chilly under his bare feet, but he didn't care. He was free again.

"Doc? Beckett? McKay, you here?" He announced over the quiet of the infirmary. That was a new one; he didn't ever remember the infirmary being this quiet. A rush of panic washed over him as he realized that this wasn't the infirmary at all. _He was back in_.

"John Sheppard." Veya stepped forward, dressed as a member of the Atlantis expedition team. She glanced down at her uniform, "This is not quite the same construct as the AR environment, but similar, where we can interact between the planes of existence. I thought this would help."

"Help with what? Pissing me off again? What the hell is going on? Tell me the truth this time. How did I get back here?" He was vibrating with frustration as the return to this scene with Veya.

"John, you are very close to physical death now. I know that you did not want to make the choice last time we spoke, your mind wasn't ready. I tried to help you the first time, to help you disengage from the system. It was too late. Your brain has been damaged by the AR environment. It was designed for our physiology, not human. Your possession of the gene helped you to survive as long as you did, but there's nothing more your people can do for you. Your Dr. McKay was not in the AR environment as long or as deep as you were, not having the gene to fully engage the interaction. I'm sorry, John."

He sat down hard on a nearby chair, the wind knocked out of him. He was having a really hard time accepting that this time, this was it_. His end_. "I need to speak with Rodney."

"John, you cannot interact with your team members any more. You are different now."

"He had been in here with us before, I need to speak with him before I go, make them understand. Please." He had to speak to Rodney and let him know that he had to go and it wasn't his fault. Atlantis would go on without him. He swallowed at that thought, he didn't want to believe it, but it was true. He was only one man, not much when compared to a whole universe.

"John, you will not be abandoning them completely. You will be able to protect them in a new way. You will be able to check in on them from time to time. You will not be able to contact them or influence them directly, but you will be able to see that they will be all right. You will ascend with us and then will understand much more than you ever thought possible and become much more than you are." Veya faded out and a light hovered around the entrance to the door. "Rodney will be here when he next falls asleep, there is a weaker barrier between the two planes at that time. Speak with him as you must and then come to the Gate room. We will leave from there. Good luck, Colonel."

"Thank you, Veya." He didn't know how it happened, but a peace descended upon him and he started to accept his new fate. He would share with Rodney what was going to happen and he would move on. They would be fine without him. He sat on the edge of his bed and waited.

Several hours later, Rodney found himself staring at the same screen for the twentieth time. His coffee cup was empty as was the decanter on the corner filing cabinet. He could barely keep his eyes open. He would take a short power nap, then be a little fresher to take a new look at these…

He didn't even finish his thought before he found himself in the infirmary. It was quiet and no one seemed to be around except for Sheppard who was sitting on one of the beds. "Colonel!" Rodney squealed before he could help himself.

"Rodney, is that you?" John was genuinely surprised that Rodney had actually showed up. "Thank god. Now we don't have much time, so close your mouth and get over here."

"Wha…? Where are we, are we back in the AR?"

"Well, sort of. I'm talking with you now because you fell asleep. No, this isn't a dream, at least I hope not. I need to tell you a few things before I go."

"Go? Go where? What are talking about?" Rodney felt the panic rising in his chest.

"Look, Rodney, I don't have time to talk you off the ledge right now. So, just shut up and listen, okay? I'll answer your questions later." John pulled him to a set of chairs in the lobby. "Okay, this is sort of an AR. From what I can tell, it's a place between planes of existence or something like that. It seems that I'm going tot have to ascend no matter if I wanted to or not. Veya says it's necessary to help Atlantis. The AR caused brain damage that I can never wake up from, do you understand? I can't come back. This is it.'

"What, it? I've been working on a way to get you back. You just have to hang on a little bit longer, can you do that?" Rodney began wringing his hands unconsciously.

John put a hand on Rodney's shoulder. "Look, I know you've been killing yourself to save me. You don't need to anymore, I'll be fine. I want you to tell everyone that I'll be okay. I don't need you or Elizabeth feeling guilty over this, understand? I will be around. You'll all be fine."

"Why don't you just wake up and tell them yourself? You can ascend some other time, like when you're good and old. How about that, huh?" Rodney blinked back moisture that was beginning to form in his eyes.

"Rodney, I just wanted to let you know how much I appreciated everything you've done for this expedition, and for me. I think of you as a brother. An ego-maniacal, over-controlling, hyper-sensitive brother, but brother. I need to know that you will be okay."

"I think of you as a brother, too, a hard-headed, stubborn mule of a brother. I can't believe that you are lying down for this. I've never known you to go down without a fight." Rodney told John.

"I can't fight this, McKay! I tried and failed. This is my last chance to make you understand that I'm not coming back!" He stood up quickly.

Rodney stood up and stared into the Colonel's eyes. "Just who are you trying to convince?"

"Dammit, Rodney! I don't want to die! I don't have any power over this. You have to know when to accept your fate and move on! I just need you to do that for me. Help the others. I've got to go now. Please tell them that it was an honor to serve…"

"..with them." Those words echoed in his ears as he woke up with a stiff neck and his computer keys embedded in his cheek. "No!" He took off towards the infirmary.

7


	13. Chapter 13

**Part XIII:**

**(A/N: This is the third to last chapter of the story. I wanted to thank all of you who have stuck with me through this whole story; it's been over a year and a half in the making! Thanks for all of your reviews _(I live for them_) and please check in on me from time to time to read the new stories. Save Stargate!). Warning: Character death (sort of).**

He crashed headlong into Elizabeth on the way and knocked the two of them to the floor. "Rodney, what's wrong?" She asked, eyes full of concern.

"Sheppard is dying. We have to get him before it's too late!" Rodney took off again, with Elizabeth not far behind.

The scene they saw when they arrived stopped them dead in their tracks. Dr. Beckett, Teyla, Ronon, and the rest of the medical team were staring at an empty bed, one that Colonel Sheppard used to occupy.

Carson looked up at Elizabeth with his eyes wet with unshed tears. "He's gone."

Teyla collapsed into Ronon's arms and Elizabeth slumped slightly before she could steel herself to the announcement. "What happened?" Rodney ground out, trying desperately to keep his voice from breaking.

"He..he seemed to be stirring. We thought he was waking up, but all of his vitals started dropping slowly, like he was slipping into a coma. He got this peaceful look on his face and blew out one last breath against the ventilator. His body seemed to disintegrate into a ball of light and then disappeared." Carson sat on the bed as he completed his summary, not quite believing what he had witnessed.

"He ascended. He told me he was going to go a few minutes ago." Elizabeth looked at Rodney like he had just grown a third arm. "I fell asleep in my lab but then seemed to wake up here, in the infirmary. John said that he had to ascend, that we would all be fine without him, but he could never wake up. Brain damage caused by the pod or some such nonsense. He wouldn't fight for himself! Goddamn it! Goddamn him and his goddamned hero complex!" Rodney took a vicious swipe at the tears that had betrayed his stoic façade and slipped down his cheeks.

"He is not dead, he has ascended. He is now with the Ancients and is part of the knowledge of the universe. We can mourn his loss to us, but we can rejoice in his addition to the universe." Teyla said quietly, openly crying. Ronon continued to hold her hand, but said nothing. His face did not betray any emotion.

"I will let the crew of Atlantis and the SGC know the news. We will have a memorial in a few days." Elizabeth told the group as evenly as she could. She felt as if one of her arms was cut off. She looked towards the doors, hoping that if she wished hard enough, John would walk through with a trademark smile on his face, telling them all it was a mistake. _God, she would have given anything for that_.

John made his way to the Gate room as instructed by Veya. She was waiting for him by the Gate. She smiled slightly at his presence. "Come, John, it is time." She extended her hand.

He nodded, but did not respond. He glanced around the Gate room for the last time and made his way to the open Gate. He watched as she passed through the Event Horizon and he followed. In that second, he thought back on all of his experiences that he had on Atlantis, all the great people that he would never forget. He had changed from that rebellious soldier who had been banned to the Antarctica base, the man whose buddies had been killed in front of him in Afghanistan, who had devolved into a Wraith-like insect, and who had made the first lasting relationships of his life. He _needed_ more time to explore what could have been with Teyla, what he could have achieved with the Wraith and other things they hadn't even thought of yet in the Pegasus Galaxy. This was one scrape he couldn't get out of, couldn't stop with a disarming smile or a hastily-constructed get-away plan.

_Welcome to the first day of the rest of your life_. He almost laughed at himself when that cliché entered his mind. What a crock! All he could hope for was to do a _Daniel Jackson_ and get sent back sometime. He only hoped that he could do some good for Atlantis in his new state and that he would actually remember why has was so concerned about them in the first place.

Elizabeth sat in her office, feeling numb and mostly surreal about John being gone. She could almost just imagine that he was an on an extended mission and that he would be back in a few weeks. She could very easily fall into that trap. Never mourning, never letting herself feel anything. _Change was hard_, isn't that what she's always been told? _Loss was even harder_. She could be clinical about all of this, philosophical about the circle of life and all that shit. _John couldn't be gone!_ She felt herself start to break down inside and she stopped herself. _This was no time to go to pieces. There will be plenty of time for that later, like every day after today. _

The two days leading up to Lt. Colonel John Sheppard's service were a blur for everyone. The _Daedalus_ was scheduled to arrive at 1400 hours, an hour before the service. General Jack O'Neill, Colonel Samantha Carter and Dr. Daniel Jackson as well as several other officers that John had served with (and had security clearance) were aboard. A general pall had descended over Atlantis and Elizabeth felt as if she would never be able to smile or enjoy anything ever again. Colonel Caldwell had actually been _nice_ to her for God's sake. Rodney hadn't left his quarters since John... since John _left_. No attempts to talk with him had been successful. She had a feeling that Kate Heightmeyer would have her work cut out for her for years to come. It really was true that you never really know what you had until it was gone. She fussed over the eulogy for the hundredth time and looked up when she heard a light tap at her office door.

"Elizabeth?" Carson asked quietly. "Are you ready?"

"Is it time already? Am I Rready? No. But I'm coming. Thanks, Carson." She stopped and looked at him sharply. She had been so wrapped up in her own pain that she hadn't thought about what Carson was going through. "How are you holding up?"

The medical doctor shook his head and looked at the floor. "I'm coping, I guess. This is really hard, harder than I ever thought possible. He was like family to me, to all of us. How do you say goodbye to family forever?" He pulled Elizabeth's hand into his own and patted it gently as he placed in the crook of his arm. "C'mon, they're waiting for you." He lead her out of her quarters and towards the Gate room.

Elizabeth blinked back new tears that formed in her eyes and followed her teammate. She walked onto the upper level overlooking the Gate room. Teyla and Ronon were standing to her left side, Rodney and Carson to her right. She smiled briefly at her team to bolster herself and to show her affection. They all smiled back. She surveyed the group that had gathered below her. All of Atlantis, including all the Athosians who could travel.

"Dearest friends of Lieutenant Colonel John Sheppard, thank you for being here. Today we gather to honor a great man and acknowledge our opportunity to have known this man, to share our experiences…."

Rodney barely heard Elizabeth's words because his own thoughts were roaring loudly in his head. He kept going back and forth about what else he could have done, what John could have or anyone else could have done to prevent this _loss_. He kept coming up with nothing that had been in their control, but that didn't stop him from obsessing about it. He scanned the crowd below and noticed that the crowd included military and scientific members alike and they were mixed in together. Not separated out by interests, comfort level, position, etc. like he'd seen at countless meetings at countless other facilities. He knew that John was integral in creating that environment and the feeling of equality between the two groups. He didn't mind taking a little credit for that himself. He was going to recognize the loss of John and use it as a catalyst to redouble his efforts to understand Ancient technology. It wasn't like he couldn't have done it before; but now, he had a timeline that he was going to impose on himself_. To prevent this from happening to anyone else. _

Teyla felt as if something in her had been extinguished, that her fire was now a pile of smoldering embers. She stood next to Ronon and held his hand tightly, as if she could bring back John just by wishing hard enough. She knew in her mind that he was in a better place, and that he would be able to do so much more for the universe in his new form. In her heart, she knew she lost someone very special whom she would never see again. She closed her eyes and could imagine him smiling at her, fighting with all of his effort with the sticks in the gym, listening to her intently when she spoke of her home world, and defending her to anyone who lost confidence in her during the Wraith telepathy incidents. This was a man who was fiercely loyal, undeniably gentle, and unquestionably loving. _Her equal_. She glanced over at Ronon and he squeezed her hand. John had given Ronon a chance that not too many would have.

Ronon had stopped listening when Elizabeth began her speech because he wasn't one for ceremony and ritual. Sheppard was gone no matter what they did. He knew that Sheppard had been a stand-up man, someone who had saved his life. He would not ever forget that. He would stay and protect Sheppard's Atlantis for as long as they would have him. He wondered briefly if they would keep him around after Sheppard was gone, but he knew that his _family _would never abandon him, especially not now. Teyla was obviously grieving and he would what he could to help her through this. He had lost his entire family after the Wraith and knew the keenness of that loss. How it bit into your soul and cut you open. How it made you feel as if you could never survive this pain. But he had and he would again. He would be changed and he would carry that with him for the rest of his life.

Carson Beckett stood as a testament to his own failure. He let Sheppard die. He couldn't save and keep the man he thought would never die around to continue saving the galaxy. He looked around at the rest of the people who depended on him to keep them alive and well. He shook his head and hoped to whoever was listening that he wouldn't fail again.


End file.
